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1.
  • Sidstedt, Maja, et al. (författare)
  • Digital PCR inhibition mechanisms using standardized inhibitors representing soil and blood matrices
  • 2016
  • Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
    • Digital PCR (dPCR) enables absolute quantification of nucleic acids by partitioning the sample into hundreds or thousands of minute reactions. By assuming a Poisson distribution for the number of DNA fragments present in each chamber, the DNA concentrationis determined without the need for a standard curve. However, when analyzing nucleic acids from complex matrices such as soil and blood, the dPCR quantification can be biased due to the presence of inhibitory compounds. Here, we present how certain inhibitors disturb dPCR quantification and suggest solutions to these problems. Furthermore, we use real-time PCR, dPCR and isothermal titration calorimetry as tools to elucidate the mechanisms underlying the PCR inhibition. The impact of impurities on dPCR quantification was studied using humic acid as a model inhibitor. We show that the inhibitor-tolerance differs greatly for three different DNA polymerases, illustrating the importance of choosing a DNA polymerase-buffer system that is compatible with the samples to be analysed. Various inhibitory-substances from blood were found to disturb the system in different ways. For example, hemoglobin was found to cause quenching of fluorescence and a dramatic decrease of the number of positive reactions, leading to an underestimation of DNA quantity. IgG caused an increased number of late-starters. The system was more susceptible to inhibition by IgG when single-stranded DNA was used as template, compared with double-stranded DNA. By understanding more about the mechanisms of PCR inhibitors it will be possible to design more optimal PCR chemistries, improving dPCR detection and quantification.
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2.
  • Sidstedt, Maja, et al. (författare)
  • Inhibition mechanisms of hemoglobin, immunoglobulin G, and whole blood in digital and real-time PCR
  • 2018
  • Ingår i: Analytical and Bioanalytical Chemistry. - : Springer Science and Business Media LLC. - 1618-2642 .- 1618-2650. ; 410:10, s. 2569-2583
  • Tidskriftsartikel (refereegranskat)abstract
    • Blood samples are widely used for PCR-based DNA analysis in fields such as diagnosis of infectious diseases, cancer diagnostics, and forensic genetics. In this study, the mechanisms behind blood-induced PCR inhibition were evaluated by use of whole blood as well as known PCR-inhibitory molecules in both digital PCR and real-time PCR. Also, electrophoretic mobility shift assay was applied to investigate interactions between inhibitory proteins and DNA, and isothermal titration calorimetry was used to directly measure effects on DNA polymerase activity. Whole blood caused a decrease in the number of positive digital PCR reactions, lowered amplification efficiency, and caused severe quenching of the fluorescence of the passive reference dye 6-carboxy-X-rhodamine as well as the double-stranded DNA binding dye EvaGreen. Immunoglobulin G was found to bind to single-stranded genomic DNA, leading to increased quantification cycle values. Hemoglobin affected the DNA polymerase activity and thus lowered the amplification efficiency. Hemoglobin and hematin were shown to be the molecules in blood responsible for the fluorescence quenching. In conclusion, hemoglobin and immunoglobulin G are the two major PCR inhibitors in blood, where the first affects amplification through a direct effect on the DNA polymerase activity and quenches the fluorescence of free dye molecules, and the latter binds to single-stranded genomic DNA, hindering DNA polymerization in the first few PCR cycles. [Figure not available: see fulltext.]
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3.
  • Sidstedt, Maja, et al. (författare)
  • The impact of common PCR inhibitors on forensic MPS analysis
  • 2019
  • Ingår i: Forensic Science International: Genetics. - : Elsevier BV. - 1872-4973. ; 40, s. 182-191
  • Tidskriftsartikel (refereegranskat)abstract
    • Massively parallel sequencing holds great promise for new possibilities in the field of forensic genetics, enabling simultaneous analysis of multiple markers as well as offering enhanced short tandem repeat allele resolution. A challenge in forensic DNA analysis is that the samples often contain low amounts of DNA in a background that may interfere with downstream analysis. PCR inhibition mechanisms of some relevant molecules have been studied applying e.g. real-time PCR and digital PCR. However, a detailed understanding of the effects of inhibitory molecules on forensic MPS, including mechanisms and ways to relieve inhibition, is missing. In this study, the effects of two well-characterized PCR inhibitors, humic acid and hematin, have been studied using the ForenSeq DNA Signature Prep kit. Humic acid and hematin resulted in lowered read numbers as well as specific negative effects on certain markers. Quality control of libraries with Fragment analyzer showed that increasing amounts of inhibitors caused a lowered amplicon quantity and that the larger amplicons were more likely to drop out. Further, the inhibitor tolerance could be improved 5–10 times by addition of bovine serum albumin in the initial PCR. On the contrary to the samples with inhibitors, low-template samples resulted in lowered read numbers for all markers. This difference strengthened the conclusion that the inhibitors have a negative effect on the DNA polymerase activity in the initial PCR. Additionally, a common capillary gel electrophoresis-based STR kit was shown to handle at least 200 times more inhibitors than the ForenSeq DNA Signature Prep kit. This suggests that there is room for improvement of the PCR components to ensure analytical success for challenging samples, which is needed for a broad application of MPS for forensic STR analysis.
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4.
  • Sidstedt, Maja, et al. (författare)
  • Ultrasensitive sequencing of STR markers utilizing unique molecular identifiers and the SiMSen-Seq method
  • 2024
  • Ingår i: Forensic Science International: Genetics. - : Elsevier Ireland Ltd. - 1872-4973 .- 1878-0326. ; 71
  • Tidskriftsartikel (refereegranskat)abstract
    • Massively parallel sequencing (MPS) is increasingly applied in forensic short tandem repeat (STR) analysis. The presence of stutter artefacts and other PCR or sequencing errors in the MPS-STR data partly limits the detection of low DNA amounts, e.g., in complex mixtures. Unique molecular identifiers (UMIs) have been applied in several scientific fields to reduce noise in sequencing. UMIs consist of a stretch of random nucleotides, a unique barcode for each starting DNA molecule, that is incorporated in the DNA template using either ligation or PCR. The barcode is used to generate consensus reads, thus removing errors. The SiMSen-Seq (Simple, multiplexed, PCR-based barcoding of DNA for sensitive mutation detection using sequencing) method relies on PCR-based introduction of UMIs and includes a sophisticated hairpin design to reduce unspecific primer binding as well as PCR protocol adjustments to further optimize the reaction. In this study, SiMSen-Seq is applied to develop a proof-of-concept seven STR multiplex for MPS library preparation and an associated bioinformatics pipeline. Additionally, machine learning (ML) models were evaluated to further improve UMI allele calling. Overall, the seven STR multiplex resulted in complete detection and concordant alleles for 47 single-source samples at 1 ng input DNA as well as for low-template samples at 62.5 pg input DNA. For twelve challenging mixtures with minor contributions of 10 pg to 150 pg and ratios of 1–15% relative to the major donor, 99.2% of the expected alleles were detected by applying the UMIs in combination with an ML filter. The main impact of UMIs was a substantially lowered number of artefacts as well as reduced stutter ratios, which were generally below 5% of the parental allele. In conclusion, UMI-based STR sequencing opens new means for improved analysis of challenging crime scene samples including complex mixtures.
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5.
  • Andersson, Ulrika, et al. (författare)
  • Beta-glucose 1-phosphate-interconverting enzymes in maltose- and trehalose-fermenting lactic acid bacteria.
  • 2002
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2920 .- 1462-2912. ; 4:2, s. 81-88
  • Tidskriftsartikel (refereegranskat)abstract
    • Maltose and trehalose catabolic pathways are linked through their common enzyme, beta-phosphoglucomutase, and metabolite, beta-glucose 1-phosphate, in Lactococcus lactis. Maltose is degraded by the concerted action of maltose phosphorylase and beta-phosphoglucomutase, whereas trehalose is assimilated by a novel pathway, including the recently discovered enzyme, trehalose 6-phosphate phosphorylase, and beta-phosphoglucomutase. In the present study, 40 strains of lactic acid bacteria were investigated for utilization of metabolic reactions involving beta-glucose 1-phosphate. All genera of the low G+C content lactic acid bacteria belonging to the clostridial subbranch of Gram-positive bacteria were represented in the study. The strains, which fermented maltose or trehalose, were investigated for beta-phosphoglucomutase, maltose phosphorylase and trehalose 6-phosphate phosphorylase activity, as indications of maltose and trehalose catabolic pathways involving beta-glucose 1-phosphate interconversions. Eighty per cent of all strains fermented maltose and, of these strains, 63% were shown to use a maltose phosphorylase/beta- phosphoglucomutase pathway. One-third of the strains fermenting trehalose were found to harbour trehalose 6-phosphate phosphorylase activity, and these were also shown to possess beta-phosphoglucomutase activity. Mainly L. lactis and Enterococcus faecalis strains were found to harbour the novel trehalose 6-phosphate phosphorylase/beta-phosphoglucomutase pathway. As lower beta-glucose 1-phosphate interconverting enzyme activities were observed in the majority of glucose-cultivated lactic acid bacteria, glucose was suggested to repress the synthesis of these enzymes in most strains. Thus, metabolic reactions involving the beta-anomer of glucose 1-phosphate are frequently found in both maltose- and trehalose-utilizing lactic acid bacteria.
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6.
  • Andersson, Ulrika, et al. (författare)
  • Physiological function of the maltose operon regulator, MalR, in Lactococcus lactis.
  • 2002
  • Ingår i: BMC Microbiology. - 1471-2180. ; 2
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Maltose metabolism is initiated by an ATP-dependent permease system in Lactococcus lactis. The subsequent degradation of intracellular maltose is performed by the concerted action of Pi-dependent maltose phosphorylase and beta-phosphoglucomutase. In some Gram-positive bacteria, maltose metabolism is regulated by a maltose operon regulator (MalR), belonging to the LacI-GalR family of transcriptional regulators. A gene presumed to encode MalR has been found directly downstream the maltose phosphorylase-encoding gene, malP in L. lactis. The purpose of this study was to investigate the physiological role of the MalR protein in maltose metabolism in L. lactis. RESULTS: A L. lactis ssp. lactis mutant, TMB5004, deficient in the putative MalR protein, was physiologically characterised. The mutant was not able to ferment maltose, while its capability to grow on glucose as well as trehalose was not affected. The activity of maltose phosphorylase and beta-phosphoglucomutase was not affected in the mutant. However, the specific maltose uptake rate in the wild type was, at its lowest, five times higher than in the mutant. This difference in maltose uptake increased as the maltose concentration in the assay was increased. CONCLUSION: According to amino acid sequence similarities, the presumed MalR is a member of the LacI-GalR family of transcriptional regulators. Due to the suggested activating effect on maltose transport and absence of effect on the activities of maltose phosphorylase and beta-phosphoglucomutase, MalR of L. lactis is considered rather as an activator than a repressor.
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7.
  • Andersson, Ulrika, et al. (författare)
  • Unity in organisation and regulation of catabolic operons in Lactobacillus plantarum, Lactococcus lactis and Listeria monocytogenes
  • 2005
  • Ingår i: Systematic and Applied Microbiology. - : Elsevier BV. - 0723-2020. ; 28:3, s. 187-195
  • Tidskriftsartikel (refereegranskat)abstract
    • Global regulatory circuits together with more specific local regulators play a notable role when cells are adapting to environmental changes. Lactococcus lactis is a lactic acid bacterium abundant in nature fermenting most mono- and disaccharides. Comparative genomics analysis of the operons encoding the proteins and enzymes crucial for catabolism of lactose, maltose and threhalose revealed an obvious unity in operon organisation. The local regulator of each operon was located in a divergent transcriptional direction to the rest of the operon including the transport protein-encoding genes. Furthermore, in all three operons a catabolite responsive element (CRE) site was detected inbetween the gene encoding the local regulator and one of the genes encoding ! sugar transport protein. It is evident that regardless of type of transport system and catabolic enzymes acting upon lactose, maltose and trehalose, respectively, Lc. lactis shows unity in both operon organisation and regulation of these catabolic operons. This knowledge was further extended to other catabolic operons in Lc. lactis and the two related bacteria Lactobacillus plantarum and Listeria monocytogenes. Thirty-nine catabolic operons responsible for degradation of sugars and sugar alcohols in Lc. lactis, Lb. plantarum and L. monocytogenes were investigated and the majority of those possessed the same organisation as the lactose, maltose and trehalose operons of Lc. lactis. Though, the frequency of CRE sites and their location varied among the bacteria. Both Lc. lactis and Lb. plantarum showed CRE sites in direct proximity to genes coding for proteins responsible for sugar uptake. However, in, L. monocytogenes CRE sites were not frequently found and not in the vicinity of genes encoding transport proteins, suggesting a more local mode of regulation of the catabolic operons found and/or the use of inducer control in this bacterium. © 2004 Elsevier GrnbH. All rights reserved.
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8.
  • Anrup, Roland, et al. (författare)
  • Centrala universitetsvärden hotas av bolagiseringsidén
  • 2013
  • Ingår i: Dagens nyheter. - 1101-2447.
  • Tidskriftsartikel (populärvet., debatt m.m.)abstract
    • Högskolestiftelser. Förslaget att driva svenska universitet i stiftelseform ­öppnar för bolagisering. Men det är ingen riktig utredning, utan en politisk pamflett utan ­eftertanke. Privatisering av universitet hotar både oberoendet, forskningskvaliteten och samhällsnyttan, skriver 36 forskare vid svenska högskolor och universitet.
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9.
  • Aprodu, Iuliana, et al. (författare)
  • Advanced sample preparation for the molecular quantification of Staphylococcus aureus in artificially and naturally contaminated milk.
  • 2011
  • Ingår i: International Journal of Food Microbiology. - : Elsevier BV. - 0168-1605. ; 145, s. 61-65
  • Tidskriftsartikel (refereegranskat)abstract
    • Sample treatment is an essential element when using real-time PCR for quantification of pathogens directly on food samples. This study comparatively evaluated three different principles of sample treatment, i.e. immunomagnetic separation based on phage-derived cell wall binding molecules, matrix solubilization and flotation, in order to establish their suitability for quantifying low numbers of Staphylococcus aureus in milk. All three procedures succeeded to remove S. aureus from the milk matrix, either raw or pasteurized, and, as a result of the concentration of the target cells, minimized the effect of milk associated PCR inhibitors. Sample preparation based on immunomagnetic separation albeit of being user friendly, specific and rapid, failed to allow quantification of low and medium numbers (<10(4)CFU) of S. aureus. In a mastitic milk model cell wall binding domain (CBD)-based target cell extraction revealed results most closely matching those derived from culture-based quantification. Both matrix lysis and flotation allowed quantification of S. aureus at a level of 1-10 cells per ml. Both methods resulted in higher numbers of bacterial cell equivalents (bce) than plating could reveal. Since both methods harvest cells that have been subjected to either mechanical and chemical stresses before quantification, we concluded that the higher bce numbers resulted from a disaggregation of S. aureus clusters initially present in the inoculum. Conclusively, since likely each S. aureus cell of a toxigenic strain contributes to enterotoxin production, molecular quantification could provide an even more realistic impact assessment in outbreak investigations than plating does.
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10.
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11.
  • Artin, Ingrid, et al. (författare)
  • Effects of Carbon Dioxide on Growth of Proteolytic Clostridium botulinum, Its Ability To Produce Neurotoxin, and Its Transcriptome
  • 2010
  • Ingår i: Applied and Environmental Microbiology. - 0099-2240. ; 76:4, s. 1168-1172
  • Tidskriftsartikel (refereegranskat)abstract
    • The antimicrobial gas carbon dioxide is frequently used in modified atmosphere packaging. In the present study, the effects of CO2 (10 to 70%, vol/vol) on gene expression (measured using quantitative reverse transcription-PCR and a whole-genome DNA microarray) and neurotoxin formation (measured using an enzyme-linked immunosorbent assay [ELISA]) by proteolytic Clostridium botulinum type A1 strain ATCC 3502 were studied during the growth cycle. Interestingly, in marked contrast to the situation with nonproteolytic C. botulinum types B and E, CO2 had little effect on any of these parameters. At all CO2 concentrations, relative expression of neurotoxin cluster genes peaked in the transition between exponential and stationary phases, with evidence of a second rise in expression in late stationary phase. Microarray analysis enabled identification of coding sequences whose expression profiles matched those of the neurotoxin cluster. Further research is needed to determine whether these are connected to neurotoxin formation or are merely growth phase associated.
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12.
  • Artin, Ingrid, et al. (författare)
  • Effects of carbon dioxide on neurotoxin gene expression in nonproteolytic Clostridium botulinum type E
  • 2008
  • Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 74:8, s. 2391-2397
  • Tidskriftsartikel (refereegranskat)abstract
    • Carbon dioxide is an antimicrobial gas commonly used in modified atmosphere packaging. In the present study, the effects of carbon dioxide on the growth of and neurotoxin production by nonproteolytic Clostridium botulinum type E were studied during the growth cycle. Quantitative reverse transcription-PCR and an enzyme-linked immunosorbent assay were used to quantify expression of the type E botulinum neurotoxin gene (cntE) and the formation of type E neurotoxin. The expression levels of cntE were similar in two strains, with relative expression peaking in the transition between exponential phase and stationary phase. In stationary phase, cntE mRNA expression declined rapidly. The cntE mRNA half-life was calculated to be approximately 9 minutes. Neurotoxin formation occurred in late exponential phase and stationary phase. High carbon dioxide concentrations delayed growth by increasing the lag time and decreasing the maximum growth rate. The effects of carbon dioxide concentration on relative neurotoxin gene expression and neurotoxin formation were significant. Expression of cntE mRNA and the formation of extracellular neurotoxin were twofold higher with a headspace carbon dioxide concentration of 70% (vol/vol) compared to 10% (vol/vol). This finding sheds a new, cautionary light on the potential risks of botulism associated with the use of modified atmosphere packaging. Copyright © 2008, American Society for Microbiology. All Rights Reserved.
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13.
  • Artin, Ingrid, et al. (författare)
  • First case of type E wound botulism diagnosed using real-time PCR.
  • 2007
  • Ingår i: Journal of Clinical Microbiology. - 1098-660X. ; 45:11, s. 3589-3594
  • Tidskriftsartikel (refereegranskat)abstract
    • Wound botulism is a growing problem among injecting drug users. The condition is often difficult to diagnose, with laboratory confirmation in only 50% of the cases. Here we present a real-time PCR-based method for the diagnosis of wound botulism caused by Clostridium botulinum. The assay includes an internal amplification control which is amplified simultaneously with the genes encoding neurotoxin types A, B, and E. This method was used to detect the first case of wound botulism in an injecting drug user in Sweden. In addition, to the best of our knowledge, this is the first reported case of wound botulism caused by C. botulinum type E.
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14.
  • Blixt, Y., et al. (författare)
  • Interlaboratory random amplified polymorphic DNA typing of Yersinia enterocolitica and Y. enterocolitica-like bacteria
  • 2003
  • Ingår i: International Journal of Food Microbiology. - 0168-1605 .- 1879-3460. ; 83:1, s. 15-26
  • Tidskriftsartikel (refereegranskat)abstract
    • A random amplified polymorphic DNA (RAPD) protocol was developed for interlaboratory use to discriminate food-borne Yersinia enterocolitica O:3 from other serogroups of Y. enterocolitica and from Y. enterocolitica-like species. Factors that were studied regarding the RAPD performance were choice of primers and concentration of PCR reagents (template DNA, MgCl 2, primer and Taq DNA polymerase). A factorial design experiment was performed to identify the optimal concentrations of the PCR reagents. The experiment showed that the concentration of the PCR reagents tested significantly affected the number of distinct RAPD products. The RAPD protocol developed was evaluated regarding its discrimination ability using 70 different Yersinia strains. Cluster analysis of the RAPD patterns obtained revealed three main groups representing (i) Y. pseudotuberculosis, (ii) Y. enterocolitica and (iii) Y. kristensenii, Y. frederiksenii, Y. intermedia and Y. ruckeri. Within the Y. enterocolitica group, the European serovar (O:3) and the North American serovar (O:8) could be clearly separated from each other. All Y. enterocolitica O:3 strains were found in one cluster which could be further divided into two subclusters, representing the geographical origin of the isolates. Thus, one of the subclusters contained Y. enterocolitica O:3 strains originating from Sweden, Finland and Norway, while Danish and English O:3 strains were found in another subcluster together with O:9 and O:5,27 strains. The repeatability (intralaboratory) and reproducibility (interlaboratory) of the RAPD protocol were tested using 15 Yersinia strains representing different RAPD patterns. The intralaboratory and the interlaboratory studies gave similarity coefficients of the same magnitude (generally >70%) for the individual strains. In the present study, it was shown that interreproducible RAPD results could be achieved by appropriate optimisation of the RAPD protocol. Furthermore, the study reflects the heterogeneous genetic diversity of the Y. enterocolitica species. © 2002 Elsevier Science B.V. All rights reserved.
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15.
  • Borgmästars, Emmy, et al. (författare)
  • Improved Detection of Norovirus and Hepatitis A Virus in Surface Water by Applying Pre-PCR Processing
  • 2017
  • Ingår i: Food and Environmental Virology. - : Springer Science and Business Media LLC. - 1867-0334 .- 1867-0342. ; 9:4, s. 395-405
  • Tidskriftsartikel (refereegranskat)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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16.
  • Cao, Rong, et al. (författare)
  • Elevated Enterotoxin A Expression and Formation in Staphylococcus aureus and its Association with Prophage Induction.
  • 2012
  • Ingår i: Applied and Environmental Microbiology. - 0099-2240. ; 78:14, s. 4942-4948
  • Tidskriftsartikel (refereegranskat)abstract
    • Staphylococcus aureus strains producing the bacteriophage-encoded staphylococcal enterotoxin A (SEA) were divided into two groups, high- and low-SEA-producing strains, based on the amount of SEA produced. After growth under favorable conditions in batch cultures, ten of the 21 strains tested produced more than 1,000 ng/ml SEA and nine strains produced less than 10 ng/ml SEA; two enterotoxigenic strains, MRSA252 and Newman, produced intermediate levels of SEA (around 450 ng/ml). The differences in the production of SEA were found to be associated with the expression level of sea and whether they hosted the versions sea(1) or sea(2). Furthermore, differences in the nucleotide sequence in the Siphoviridae phage region showed two clonal lineages of the high-SEA-producing strains. One of these lines was correlated with the capacity for a massive increase in SEA levels by prophage induction as demonstrated using mitomycin C (MC). This was also confirmed by the occurrence of additional sea expression presumed to be initiated by a latent phage promoter located upstream of the endogenous sea promoter. Remarkably, the SEA level was increased by up to ten fold in some strains due to prophage induction. The low-SEA-producing group and the high-SEA-producing subgroup lacking phage activated sea transcription showed no increase in SEA formation after the addition of MC. This study demonstrates that sea expression in enterotoxigenic strains is correlated with the clonal lineage of sea-encoded phages. The high-SEA-producing group, and in particular the prophage inducible sea(1) group, may be more relevant in staphylococcal food poisoning than the low-SEA-producing group, mainly harboring sea(2).
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17.
  • Cao, Rong, et al. (författare)
  • Inhibition kinetics of catabolic dehydrogenases by elevated moieties of ATP and ADP - implication for a new regulation mechanism in Lactococcus lactis
  • 2010
  • Ingår i: The FEBS Journal. - : Wiley. - 1742-464X. ; 277:8, s. 1843-1852
  • Tidskriftsartikel (refereegranskat)abstract
    • ATP and ADP inhibit, in varying degrees, several dehydrogenases of the central carbon metabolism of Lactococcus lactis ATCC 19435 in vitro, i.e. glyceraldehyde-3-phosphate dehydrogenase (GAPDH), lactate dehydrogenase (LDH) and alcohol dehydrogenase (ADH). Here we demonstrate mixed inhibition for GAPDH and competitive inhibition for LDH and ADH by adenine nucleotides in single inhibition studies. The nonlinear negative co-operativity was best modelled with Hill-type kinetics, showing greater flexibility than the usual parabolic inhibition equation. Because these natural inhibitors are present simultaneously in the cytoplasm, multiple inhibition kinetics was determined for each dehydrogenase. For ADH and LDH, the inhibitor combinations ATP plus NAD and ADP plus NAD are indifferent to each other. Model discrimination suggested that the weak allosteric inhibition of GAPDH had no relevance when multiple inhibitors are present. Interestingly, with ADH and GAPDH the combination of ATP and ADP exhibits lower dissociation constants than with either inhibitor alone. Moreover, the concerted inhibition of ADH and GAPDH, but not of LDH, shows synergy between the two nucleotides. Similar kinetics, but without synergies, were found for horse liver and yeast ADHs, indicating that dehydrogenases can be modulated by these nucleotides in a nonlinear manner in many organisms. The action of an elevated pool of ATP and ADP may effectively inactivate lactococcal ADH, but not GAPDH and LDH, providing leverage for the observed metabolic shift to homolactic acid formation in lactococcal resting cells on maltose. Therefore, we interpret these results as a regulation mechanism contributing to readjusting the flux of ATP production in L. lactis.
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18.
  • Chan, Sandy, et al. (författare)
  • Bacterial release from pipe biofilm in a full-scale drinking water distribution system
  • 2019
  • Ingår i: npj Biofilms and Microbiomes. - : Springer Science and Business Media LLC. - 2055-5008. ; 5:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Safe drinking water is delivered to the consumer through kilometres of pipes. These pipes are lined with biofilm, which is thought to affect water quality by releasing bacteria into the drinking water. This study describes the number of cells released from this biofilm, their cellular characteristics, and their identity as they shaped a drinking water microbiome. Installation of ultrafiltration (UF) at full scale in Varberg, Sweden reduced the total cell count to 1.5 × 10 3 ± 0.5 × 10 3 cells mL −1 in water leaving the treatment plant. This removed a limitation of both flow cytometry and 16S rRNA amplicon sequencing, which have difficulties in resolving small changes against a high background cell count. Following installation, 58% of the bacteria in the distributed water originated from the pipe biofilm, in contrast to before, when 99.5% of the cells originated from the treatment plant, showing that UF shifts the origin of the drinking water microbiome. The number of bacteria released from the biofilm into the distributed water was 2.1 × 10 3 ± 1.3 × 10 3 cells mL −1 and the percentage of HNA (high nucleic acid) content bacteria and intact cells increased as it moved through the distribution system. DESeq2 analysis of 16S rRNA amplicon reads showed increases in 29 operational taxonomic units (OTUs), including genera identified as Sphingomonas, Nitrospira, Mycobacterium, and Hyphomicrobium. This study demonstrated that, due to the installation of UF, the bacteria entering a drinking water microbiome from a pipe biofilm could be both quantitated and described.
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19.
  • Chan, Sandy, et al. (författare)
  • Monitoring biofilm function in new and matured full-scale slow sand filters using flow cytometric histogram image comparison (CHIC)
  • 2018
  • Ingår i: Water Research. - : Elsevier BV. - 0043-1354. ; 138, s. 27-36
  • Tidskriftsartikel (refereegranskat)abstract
    • While slow sand filters (SSFs) have produced drinking water for more than a hundred years, understanding of their associated microbial communities is limited. In this study, bacteria in influent and effluent water from full-scale SSFs were explored using flow cytometry (FCM) with cytometric histogram image comparison (CHIC) analysis; and routine microbial counts for heterotrophs, total coliforms and Escherichia coli. To assess if FCM can monitor biofilm function, SSFs differing in age and sand composition were compared. FCM profiles from two established filters were indistinguishable. To examine biofilm in the deep sand bed, SSFs were monitored during a scraping event, when the top layer of sand and the schmutzdecke are removed to restore flow through the filter. The performance of an established SSF was stable: total organic carbon (TOC), pH, numbers of heterotrophs, coliforms, E. coli, and FCM bacterial profile were unaffected by scraping. However, the performance of two newly-built SSFs containing new and mixed sand was compromised: breakthrough of both microbial indicators and TOC occurred following scraping. The compromised performance of the new SSFs was reflected in distinct effluent bacterial communities; and, the presence of microbial indicators correlated to influent bacterial communities. This demonstrated that FCM can monitor SSF performance. Removal of the top layer of sand did not alter the effluent water from the established SSF, but did affect that of the SSFs containing new sand. This suggests that the impact of the surface biofilm on effluent water is greater when the deep sand bed biofilm is not established.
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20.
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21.
  • Dahlenborg, Maria, et al. (författare)
  • Prevalence of Clostridium botulinum types B, E, and F in faecal samples from Swedish cattle.
  • 2003
  • Ingår i: International Journal of Food Microbiology. - 0168-1605 .- 1879-3460. ; 82:2, s. 105-110
  • Tidskriftsartikel (refereegranskat)abstract
    • Faeces were collected from 60 cows at three slaughterhouses situated in southern and central Sweden. The faecal samples were collected during two sampling periods over the year, summer and winter. All samples were analysed for the presence of Clostridium botulinum spores, according to a combined selection and enrichment PCR procedure. One PCR assay was specific for part of the type B neurotoxin gene, while the other assay was specific for both type E and F neurotoxin genes. The prevalence of C. botulinum in Swedish cattle was established to be 73% for non-proteolytic type B and less than 5% for types E and F. Twenty-eight (64%) of the positive faecal samples had a spore load of less than 4 spores/g. Statistical analysis (ANOVA) showed that seasonal variation (summer and winter) had a significant effect on the prevalence of C. botulinum type B in cattle, whereas the effect of geographical location of rearing of the cattle (southern and central Sweden) was less significant.
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22.
  • Dai, JY, et al. (författare)
  • Conformational cycling in beta-phosphoglucomutase catalysis: Reorientation of the beta-D-glucose 1,6-(bis) phosphate intermediate
  • 2006
  • Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 45:25, s. 7818-7824
  • Tidskriftsartikel (refereegranskat)abstract
    • Activated Lactococcus lactis beta-phosphoglucomutase (beta PGM) catalyzes the conversion of beta-D-glucose 1-phosphate (beta G1P) derived from maltose to beta-D-glucose 6-phosphate (G6P). Activation requires Mg2+ binding and phosphorylation of the active site residue Asp8. Initial velocity techniques were used to define the steady-state kinetic constants k(cat) = 177 +/- 9 s(-1), K-m = 49 +/- 4 mu M for the substrate, beta G1P and K-m = 6.5 +/- 0.7 mu M for the activator beta-D-glucose 1,6-bisphosphate (beta G1,6bisP). The observed transient accumulation of [C-14]beta G1,6bisP (12% at similar to 0.1 s) in the single turnover reaction carried out with excess beta PGM (40 mu M) and limiting [C-14]beta G1P (5 mu M) and beta G1,6bisP (5 mu M) supported the role of beta G1,6bisP as a reaction intermediate in the conversion of the, G1P to G6P. Single turnover reactions of [C-14]beta G1,6bisP with excess, beta PGM were carried out to demonstrate that phosphoryl transfer rather than ligand binding is rate-limiting and to show that the beta G1,6bisP binds to the active site in two different orientations (one positioning the C(1) phosphoryl group for reaction with Asp8, and the other orientation positioning the C(6) phosphoryl group for reaction with Asp8) with roughly the same efficiency. Single turnover reactions carried out with beta PGM, [C-14]beta G1P, and unlabeled beta G1,6bisP demonstrated complete exchange of label to the beta G1,6bisP during the catalytic cycle. Thus, the reorientation of the beta G1,6bisP intermediate that is required to complete the catalytic cycle occurs by diffusion into solvent followed by binding in the opposite orientation. Published X-ray structures of beta G1P suggest that the reorientation and phosphoryl transfer from beta G1,6bisP occur by conformational cycling of the enzyme between the active site open and closed forms via cap domain movement. Last, the equilibrium ratio of beta G1,6bisP to beta G1P plus G6P was examined to evidence a significant stabilization of beta PGM aspartyl phosphate.
  •  
23.
  • de Vin, Filip, et al. (författare)
  • Molecular and biochemical analysis of the galactose phenotype of dairy Streptococcus thermophilus strains reveals four different fermentation profiles
  • 2005
  • Ingår i: Applied and Environmental Microbiology. - 0099-2240. ; 71:7, s. 3659-3667
  • Tidskriftsartikel (refereegranskat)abstract
    • Lactose-limited fermentations of 49 dairy Streptococcus thermophilus strains revealed four distinct fermentation profiles with respect to galactose consumption after lactose depletion. All the strains excreted galactose into the medium during growth on lactose, except for strain IMDOST40, which also displayed extremely high galactokinase (GalK) activity. Among this strain collection eight galactose-positive phenotypes sensu stricto were found and their fermentation characteristics and Leloir enzyme activities were measured. As the gal promoter seems to play an important role in the galactose phenotype, the galR-galK intergenic region was sequenced for all strains yielding eight different nucleotide sequences (NS1 to NS8). The gal promoter played an important role in the Gal-positive phenotype but did not determine it exclusively. Although GalT and GalE activities were detected for all Gal-positive strains, GalK activity could only be detected for two out of eight Gal-positive strains. This finding suggests that the other six S. thermophilus strains metabolize galactose via an alternative route. For each type of fermentation profile obtained, a representative strain was chosen and four complete Leloir gene clusters were sequenced. It turned out that Gal-positive strains contained more amino acid differences within their gal genes than Gal-negative strains. Finally, the biodiversity regarding lactose-galactose utilization among the different S. thermophilus strains used in this study was shown by RAPD-PCR. Five Gal-positive strains that contain nucleotide sequence NS2 in their galR-galK intergenic region were closely related.
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24.
  • Eriksson, John, et al. (författare)
  • Comparison of genotyping methods by application to Salmonella livingstone strains associated with an outbreak of human salmonellosis
  • 2005
  • Ingår i: International Journal of Food Microbiology. - : Elsevier BV. - 0168-1605 .- 1879-3460. ; 104:1, s. 93-103
  • Tidskriftsartikel (refereegranskat)abstract
    • During 2000 and 2001, an outbreak of human salmonellosis occurred in Sweden and Norway, caused by Salmonella livingstone. In this study, the genotypic differences between three strains obtained from food sources during the outbreak, two human strains and 27 more or less unrelated strains were analysed, using the three methods; automated ribotyping, pulsed field get electrophoresis (PFGE) and randomly amplified polymorphic DNA (RAPD). Each method was evaluated regarding its discriminatory ability, reproducibility and typeability. Simpson's discriminatory index calculated for each method was 0.556 for automated ribotyping, 0.766 for PFGE and 0.236 for RAPD. The reproducibility, defined as the minimum similarity between individual replicates in a cluster analysis, was 96% for automated ribotyping and PFGE, and 90% for RAPD. All the strains were typeable with each method. When combining results for the three genotyping methods, it was found that RAPD did not increase the discriminatory index and was therefore excluded from further analysis. Using a combination of the results obtained from ribotyping and PFGE (D = 0.855), two strains that had been isolated from feed factories during 1998 were shown to be identical to the outbreak strain, indicating a possible route of contamination due to a clone of Salmonella livingstone persisting in feed producing facilities. No connection to poultry was established. (c) 2005 Elsevier B.V. All rights reserved.
  •  
25.
  • Gronlund, Hugo, et al. (författare)
  • Direct Detection Of Single-Nucleotide Polymorphisms In Bacterial DNA By SNPtrap
  • 2011
  • Ingår i: Preparative Biochemistry & Biotechnology. - : Informa UK Limited. - 1532-2297 .- 1082-6068. ; 41:2, s. 166-174
  • Tidskriftsartikel (refereegranskat)abstract
    • A major challenge with single-nucleotide polymorphism (SNP) fingerprinting of bacteria and higher organisms is the combination of genome-wide screenings with the potential of multiplexing and accurate SNP detection. Single-nucleotide extension by the minisequencing principle represents a technology that both is highly accurate and enables multiplexing. A current bottleneck for direct genome analyses by minisequencing, however, is the sensitivity, since minisequencing relies on linear signal amplification. Here, we present SNPtrap, which is a novel approach that combines the specificity and possibility of multiplexing by minisequencing with the sensitivity obtained by logarithmic signal amplification by polymerase chain reaction (PCR). We show a SNPtrap proof of principle in a model system for two polymorphic SNP sites in the Salmonella tetrathionate reductase gene (ttrC).
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26.
  • Grønlund, H., et al. (författare)
  • Microarray-based genotyping of Salmonella : Inter-laboratory evaluation of reproducibility and standardization potential
  • 2011
  • Ingår i: International Journal of Food Microbiology. - : Elsevier BV. - 0168-1605 .- 1879-3460. ; 145:SUPPL. 1, s. S79-S85
  • Tidskriftsartikel (refereegranskat)abstract
    • Bacterial food-borne infections in humans caused by Salmonella spp. are considered a crucial food safety issue. Therefore, it is important for the risk assessments of Salmonella to consider the genomic variation among different isolates in order to control pathogen-induced infections. Microarray technology is a promising diagnostic tool that provides genomic information on many genes simultaneously. However, standardization of DNA microarray analysis is needed before it can be used as a routine method for characterizing Salmonella isolates across borders and laboratories. A comparative study was designed in which the agreement of data from a DNA microarray assay used for typing Salmonella spp. between two different labs was assessed. The study was expected to reveal the possibility of obtaining the same results in different labs using different equipment in order to evaluate the reproducibility of the microarray technique as a first step towards standardization. The low-density array contains 281 57-60-mer oligonucleotide probes for detecting a wide range of specific genomic marker genes associated with antibiotic resistance, cell envelope structures, mobile genetic elements and pathogenicity. Several critical methodology parameters that differed between the two labs were identified. These related to printing facilities, choice of hybridization buffer, wash buffers used following the hybridization and choice of procedure for purifying genomic DNA. Critical parameters were randomized in a four-factorial experiment and statistical measures of inter-lab consistency and agreement were performed based on the kappa coefficient. A high level of agreement (kappa = 0.7-1.0) in microarray results was obtained even when employing different printing and hybridization facilities, different procedures for purifying genomic DNA and different wash buffers. However, less agreement (Kappa = 0.2-0.6) between microarray results were observed when using different hybridization buffers, indicating this parameter as being highly critical when transferring a standard microarray assay between laboratories. In conclusion, this study indicates that DNA microarray assays can be reproduced in at least two different facilities, which is a pre-requisite for the development of standard guidelines. © 2010 Elsevier B.V.
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27.
  • Hedman, Johannes, et al. (författare)
  • Improved forensic DNA analysis through the use of alternative DNA polymerases and statistical modeling of DNA profiles
  • 2009
  • Ingår i: BIOTECHNIQUES. - : Eaton Publishing. - 0736-6205 .- 1940-9818. ; 47:5, s. 951-958
  • Tidskriftsartikel (refereegranskat)abstract
    • DNA evidence, linking perpetrators to crime scenes, is central to many legal proceedings. However, DNA samples from crime scenes often contain PCR-inhibitory substances, which may generate blank or incomplete DNA profiles. Extensive DNA purification can be required to rid the sample of these inhibitors, although these procedures increase the risk of DNA loss. Most forensic laboratories use commercial DNA amplification kits (e.g., AmpFlSTR SGM Plus) with the DNA polymerase AmpliTaq Gold as the gold standard. Here, we show that alternative DNA polymerase-buffer systems can improve the quality of forensic DNA analysis and efficiently circumvent PCR inhibition in crime scene samples, without additional sample preparation. DNA profiles from 20 of 32 totally or partially inhibited crime scene saliva samples were significantly improved using Bio-X-Act Short, ExTaq Hot Start, or PicoMaxx High Fidelity instead of AmpliTaq Gold. A statistical model for unbiased quality control of forensic DNA profiles was developed to quantify the results. Our study demonstrates the importance of adjusting the chemistry of the PCR to enhance forensic DNA analysis and diagnostic PCR, providing an alternative to laborious sample preparation protocols.
  •  
28.
  • Hedman, Johannes, et al. (författare)
  • Pre-PCR processing in bioterrorism preparedness : improved diagnostic capabilities for laboratory response networks
  • 2013
  • Ingår i: Biosecurity and bioterrorism. - : Mary Ann Liebert. - 1538-7135 .- 1557-850X. ; 11:S1, s. S87-S101
  • Tidskriftsartikel (refereegranskat)abstract
    • Diagnostic DNA analysis using polymerase chain reaction (PCR) has become a valuable tool for rapid detection of biothreat agents. However, analysis is often challenging because of the limited size, quality, and purity of the biological target. Pre-PCR processing is an integrated concept in which the issues of analytical limit of detection and simplicity for automation are addressed in all steps leading up to PCR amplification—that is, sampling, sample treatment, and the chemical composition of PCR. The sampling method should maximize target uptake and minimize uptake of extraneous substances that could impair the analysis—so-called PCR inhibitors. In sample treatment, there is a trade-off between yield and purity, as extensive purification leads to DNA loss. A cornerstone of pre-PCR processing is to apply DNA polymerase-buffer systems that are tolerant to specific sample impurities, thereby lowering the need for expensive purification steps and maximizing DNA recovery. Improved awareness among Laboratory Response Networks (LRNs) regarding pre-PCR processing is important, as ineffective sample processing leads to increased cost and possibly false-negative or ambiguous results, hindering the decision-making process in a bioterrorism crisis. This article covers the nature and mechanisms of PCR-inhibitory substances relevant for agroterrorism and bioterrorism preparedness, methods for quality control of PCR reactions, and applications of pre-PCR processing to optimize and simplify the analysis of various biothreat agents. Knowledge about pre-PCR processing will improve diagnostic capabilities of LRNs involved in the response to bioterrorism incidents.
  •  
29.
  • Hedman, Johannes, et al. (författare)
  • Synergy between DNA polymerases increases polymerase chain reaction inhibitor tolerance in forensic DNA analysis
  • 2010
  • Ingår i: Analytical Biochemistry. - - : Elsevier Inc.. - 0003-2697 .- 1096-0309. ; 405, s. 192-200
  • Tidskriftsartikel (refereegranskat)abstract
    • The success rate of diagnostic polymerase chain reaction (PCR) analysis is lowered by inhibitory substancespresent in the samples. Recently, we showed that tolerance to PCR inhibitors in crime scene salivastains can be improved by replacing the standard DNA polymerase AmpliTaq Gold with alternative DNApolymerase–buffer systems (Hedman et al., BioTechniques 47 (2009) 951–958). Here we show thatblending inhibitor-resistant DNA polymerase–buffer systems further increases the success rate of PCRfor various types of real crime scene samples showing inhibition. For 34 of 42 ‘‘inhibited” crime scenestains, the DNA profile quality was significantly improved using a DNA polymerase blend of ExTaq HotStart and PicoMaxx High Fidelity compared with AmpliTaq Gold. The significance of the results was confirmedby analysis of variance. The blend performed as well as, or better than, the alternative DNA polymerasesused separately for all tested sample types. When used separately, the performance of the DNApolymerases varied depending on the nature of the sample. The superiority of the blend is discussed interms of complementary effects and synergy between the DNA polymerase–buffer systems.
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30.
  • Hedman, Johannes, et al. (författare)
  • Validation guidelines for PCR workflows in bioterrorism preparedness, food safety and forensics
  • 2018
  • Ingår i: Accreditation and Quality Assurance. - : Springer Science and Business Media LLC. - 0949-1775 .- 1432-0517. ; 23:3, s. 133-144
  • Tidskriftsartikel (refereegranskat)abstract
    • The polymerase chain reaction (PCR) is the backbone of contemporary DNA/RNA analysis, ideally enabling detection of one or just a few target molecules. However, when analysing food or forensic samples the analytical procedure is often challenged by low amounts of poor quality template molecules and complex matrices. Applying optimised and validated methods in all steps of the analysis workflow, i.e. sampling, sample treatment, DNA/RNA extraction and PCR (including reverse transcription for RNA analysis), is thus necessary to ensure the reliability of analysis. In this paper, we describe how in-house validation can be performed for the different modules of the diagnostic PCR process, providing practical examples as tools for laboratories in their planning of validation studies. The focus is analysis of heterogeneous samples with interfering matrices, with relevance in food testing, forensic DNA analysis, bioterrorism preparedness and veterinary medicine. Our objective is to enable rational in-house validation for reliable and swift quality assurance when results are urgent, for example in the event of a crisis such as a foodborne outbreak or a crime requiring the analysis of a large number of diverse samples. To that end, we explain the performance characteristics associated with method validation from a PCR and biological sample matrix perspective and suggest which characteristics to investigate depending on the type of method to be validated. Also, we include a modular approach to validation within the PCR workflow, aiming at efficient validation and a flexible use of methods.
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31.
  • Hoorfar, Jeffrey, et al. (författare)
  • Diagnostic PCR: validation and sample preparation are two sides of the same coin
  • 2004
  • Ingår i: APMIS : acta pathologica, microbiologica, et immunologica Scandinavica. - : Wiley. - 1600-0463. ; 112:11-12, s. 808-814
  • Forskningsöversikt (refereegranskat)abstract
    • Increased use of powerful PCR technology for the routine detection of pathogens has focused attention on the need for international validation and preparation of official non-commercial guidelines. Bacteria of epidemiological importance should be the prime focus, although a "validation infrastructure" once established could easily be adapted for PCR-based detection of viruses and parasites. The aim of standardization should be the widespread adoption of diagnostic PCR for routine pathogen testing. European experience provides the impetus for realization of this vision through preparation of quantitative reference DNA material and reagents, production of stringent protocols and tools for thermal cycler performance testing, uncomplicated sample preparation techniques, and extensive ring trials for assessment of the efficacy of selected matrix/pathogen detection protocols.
  •  
32.
  • Hunt, Karen, et al. (författare)
  • Classical enterotoxins of coagulase-positive Staphylococcus aureus isolates from raw milk and products for raw milk cheese production in Ireland
  • 2012
  • Ingår i: Dairy Science & Technology. - : Springer Science and Business Media LLC. - 1958-5586 .- 1958-5594. ; 92:5, s. 487-499
  • Tidskriftsartikel (refereegranskat)abstract
    • Toxin-producing Staphylococcus aureus can be present in raw milk and therefore in cheese made from raw milk. To determine the number and type of toxin producers in raw milk used for raw milk cheese production in Ireland, 117 samples of raw milk and related products from five raw milk suppliers, to four raw milk cheesemakers in the South of Ireland, were analysed for coagulase positive S. aureus. Enumeration, using ISO 688-2 and plating on Baird Parker Rabbit Plasma Fibrinogen selective agar showed samples were within limits set by EC regulations. Isolates (151 from 81 positive samples) were characterised for production of staphylococcal enterotoxins (SEs) SEA, SEB, SEC and SED by reverse passive latex agglutination (SET-RPLA) and by multiplex polymerase chain reaction for the sea, seb, sec, sed and see genes. The results showed 83.2% of the isolates did not contain the se genes or the toxin producing capability tested for. From only one supplier, 26 isolates contained the sec gene and produced SEC. Within these 26 isolates, there were only two PFGE types. One SEC-producing isolate showed no toxin production when grown in sterile 10% reconstituted skim milk at 10 degrees C and 12 degrees C for 96 and 74 h, respectively. Low concentrations of SEC were produced at 14 degrees C and 16 degrees C after 74 and 55 h, respectively. The results of this survey indicate that milk used for raw milk cheese production in Ireland poses a limited risk to public health, although further studies on occurrence of toxin producing S. aureus should be undertaken.
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33.
  • Jannasch, Patric, et al. (författare)
  • Kamratgranskning av muntliga gruppresentationer: pålitlighet och effekter på studenternas lärande
  • 2009
  • Ingår i: Proceeding från Den 2:a Utvecklingskonferensen för Sveriges ingenjörsutbildningar.
  • Konferensbidrag (refereegranskat)abstract
    • Det finns goda skäl till att engagera studenterna i kamratbedömning vid både formativ och summativ examination. Vi har under kursen Molekylär Cellbiologi för Ekosystemvetare vid LTH undersökt studenternas förmåga att bedöma muntliga projektredovisningar och jämfört den med lärarnas. Under kursen genomförde studenterna ett litteraturprojekt där en muntlig gruppredovisning med efterföljande kamratdiskussion och försvar bedömdes och poängsattes av en opponerande studentgrupp och ett lärarlag. Vår undersökning visade att studenternas poängbedömning stämde väl överens med lärarlagets, både med avseende på medelvärde och spridning. Små skillnader visade sig i bedömningen av ”faktainnehåll” och ”samarbete” där lärarlaget gav ett något mer positivt omdöme, och i bedömning av ”försvar” där studentgrupperna gav lite högre poäng. En undersökning av studenternas attityder och upplevelser i samband med kamratgranskningen visade att presenterande studenter upplevde sig rättvist bedömda, men att några granskande studenter kände lite obehag och osäkerhet inför kamratbedömningen. Vidare upplevde både lärare och studenter att lärandet om ämnet, lärandeprocessen och examinationsprocessen gynnades av kamratgranskningen och kamratdiskussionerna. Sammanfattningsvis visade våra resultat att kamratgranskningen fungerade väl, och att studenterna behöver utbildning och tydlig information om bedömningskriterier och motiven för granskningsprocessen så att de kan känna sig trygga, framför allt i granskarrollen.
  •  
34.
  • Jannasch, Patric, et al. (författare)
  • Kamratgranskning och kamratdiskussion vid bedömning av muntliga gruppresentationer: pålitlighet och effekter på studenternas lärande
  • 2009
  • Ingår i: Proceedings från Lunds universitets andra utvecklingskonferens.
  • Konferensbidrag (refereegranskat)abstract
    • Det finns goda skäl till att engagera studenterna i deras egen bedömning vid både formativ och summativ examination. Vi har under kursen Molekylär Cellbiologi för Ekosystemvetare vid LTH undersökt studenternas förmåga att bedöma muntliga projektredovisningar och jämfört den med lärarnas. Under kursen genomförde studenterna ett projekt där en muntlig gruppredovisning med efterföljande kamratdiskussion och försvar bedömdes och poängsattes av en opponerande studentgrupp och ett lärarlag. Vår undersökning visade att studenternas poängbedömning stämde väl överens med lärarlagets, både med avseende på medelvärde och spridning. Små skillnader visade sig i bedömningen av ”faktainnehåll” och ”samarbete” där lärarlaget gav ett något mer positivt omdöme, och i bedömning av ”försvar” där studentgrupperna gav lite högre poäng. En undersökning av studenternas attityder och upplevelser i samband med kamratgranskningen visade att presenterande studenter upplevde sig rättvist bedömda, men att några granskande studenter kände lite obehag och osäkerhet inför kamratbedömningen. Vidare upplevde både lärare och studenter att lärandet om både ämnet, lärandeprocessen och bedömningsprocessen gynnades av kamratgranskningen och kamratdiskussionerna. Sammanfattningsvis visade våra resultat att kamratgranskningen fungerade väl, och att studenterna behöver utbildning och tydlig information om bedömningskriterier och motiven för granskningsprocessen så att de kan känna sig trygga, framför allt i granskarrollen.
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35.
  • Knutsson, Rickard, et al. (författare)
  • Development of a PCR-compatible enrichment medium for Yersinia enterocolitica: amplification precision and dynamic detection range during cultivation
  • 2002
  • Ingår i: International Journal of Food Microbiology. - 0168-1605. ; 72:3, s. 185-201
  • Tidskriftsartikel (refereegranskat)abstract
    • A Yersinia PCR-Compatible Enrichment (YPCE) medium was developed, which removes the necessity for sample pretreatment before PCR-based detection of Yersinia enterocolitica. The medium was designed through a sequence of independent screening and factorial design experiments to study the PCR inhibition and growth characteristics of medium components. The compatibility of the YPCE medium was evaluated using real-time PCR. The real-time PCR assay, based on the fluorescent double-stranded DNA binding dye SYBR green, generated approximately a 4-log linear range of amplification and in the range of 10(5)-10(8) (CFU/ml), the coefficient of variation <5%. When a background flora was present at concentrations greater than or equal to10(6) (CFU/ml), the DNA amplification was influenced and a change in the log-linear slope leading to a lower amplification efficiency was observed. To study the dynamic detection range and relative amplification precision during enrichment, Y. enterocolitica and background flora were inoculated at various concentrations. It was possible to detect inoculation concentrations of 10(1) (CFU/ml) Y enterocolitica in the presence of at least an inoculation concentration of 10(3) (CFU/ml) of an undefined background flora and the optimal conditions for sample withdrawal was in the range of 9 to 18 h enrichment. The YPCE medium can, especially for swab samples, form part of a simple analysis procedure allowing high throughput PCR. (C) 2002 Elsevier Science B.V. All rights reserved.
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36.
  • Knutsson, Rickard, et al. (författare)
  • Evaluation of selective enrichment PCR procedures for Yersinia enterocolitica.
  • 2002
  • Ingår i: International Journal of Food Microbiology. - 0168-1605 .- 1879-3460. ; 73:1, s. 35-46
  • Tidskriftsartikel (refereegranskat)abstract
    • Four enrichment PCR protocols for detecting unlysed cells of pathogenic Yersinia enterocolitica were studied. First, the probability of detecting Y. enterocolitica cells of known concentrations by a multiplex PCR assay was determined, and it was found to follow a logistic regression model. From this model, the probability of detecting Y enterocolitica at a specific concentration could be estimated; for example, the detection probability of 10(4) CFU/ml was estimated to be 85.4%. The protocols were evaluated on enrichment cultures inoculated with 10(2) CFU/ml Y. enterocolitica and 10(2)-10(6) CFU/ml of a defined background flora. For each protocol, the time for sample withdrawal and the presence of background flora were studied with respect to PCR detection. The optimal point in time of sample withdrawal was found to be different for each protocol employed. Early detection was favoured by concentrating the target cells, and the most rapid PCR detection of Y. enterocolitica was achieved with enrichment in Yersinia-PCR-compatible-enrichment (YPCE) medium for 3 h at 25 degrees C, followed by a centrifugation prior to PCR analysis. For detection of Y. enterocolitica in the presence of high concentrations (10(6) CFU/ml) of background flora, a long incubation time followed by density centrifugation and a dilution step was most successful. The protocol that gave the most reliable PCR detection in the presence of 10(6) CFU/ml background flora included 24 h incubation in Yersinia-selective-enrichment (YSE) broth at 25 degrees C, followed by Percoll density centrifugation, and a 100 times dilution prior to PCR analysis.
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37.
  • Knutsson, Rickard, et al. (författare)
  • Modeling of 5′ nuclease real-time responses for optimization of a high-throughput enrichment PCR procedure for Salmonella enterica
  • 2002
  • Ingår i: Journal of Clinical Microbiology. - 0095-1137 .- 1098-660X. ; 40:1, s. 52-60
  • Tidskriftsartikel (refereegranskat)abstract
    • The performance of a 5′ nuclease real-time PCR assay was studied to optimize an automated method of detection of preenriched Salmonella enterica cells in buffered peptone water (BPW). The concentrations and interactions of the PCR reagents were evaluated on the basis of two detection responses, the threshold cycle (Cτ) and the fluorescence intensity by a normalized reporter value (ΔRn). The Cτ response was identified as the most suitable for detection modeling to describe the PCR performances of different samples. DNA extracted from S. enterica serovar Enteritidis was studied in double-distilled H2O (ddH2O) and in two different enrichment media (brain heart infusion and BPW) with two PCR mixtures based on AmpliTaq Gold or rTth. A descriptive model was proposed and fitted to the available experimental data. Equivalent PCR performances for the two PCR mixtures were obtained when DNA was diluted in ddH2O. However, the level of detection of DNA was affected when BPW was present during amplification. Use of the rTth mixture generated a 1-log-unit wider linear range of amplification, and the DNA detection levels were 2 × 10-12 g/microwell for the rTth mixture and 2 × 10-12 g/microwell for the AmpliTaq Gold mixture. To verify the improved amplification capacity of the rTth mixture, BPW was inoculated with 1 CFU of S. enterica serovar Enteritidis per ml and the mixture was incubated at 30°C. Samples for PCR were withdrawn every 4 h during a 36-h enrichment. Use of the rTth mixture resulted in an earlier PCR detection during enrichment than use of the AmpliTaq Gold mixture. For accurate detection (Cτ ≤ 30) of S. enterica serovar Enteritidis inoculated in BPW, the rTth mixture required 8.4 h of enrichment, while the AmpliTaq Gold mixture needed 11.6 h. In conclusion, the principle applied can improve the methodology of 5′ nuclease real-time PCR for numerical optimization of sample pretreatment strategies to provide automated diagnostic PCR procedures.
  •  
38.
  • Laadan, Boaz, et al. (författare)
  • Furaldehyde substrate specificity and kinetics of Saccharomyces cerevisiae alcohol dehydrogenase 1 variants
  • 2014
  • Ingår i: Microbial Cell Factories. - : Springer Science and Business Media LLC. - 1475-2859. ; 13
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: A previously discovered mutant of Saccharomyces cerevisiae alcohol dehydrogenase 1 (Adh1p) was shown to enable a unique NADH-dependent reduction of 5-hydroxymethylfurfural (HMF), a well-known inhibitor of yeast fermentation. In the present study, site-directed mutagenesis of both native and mutated ADH1 genes was performed in order to identify the key amino acids involved in this substrate shift, resulting in Adh1p-variants with different substrate specificities. Results: In vitro activities of the Adh1p-variants using two furaldehydes, HMF and furfural, revealed that HMF reduction ability could be acquired after a single amino acid substitution (Y295C). The highest activity, however, was reached with the double mutation S110P Y295C. Kinetic characterization with both aldehydes and the in vivo primary substrate acetaldehyde also enabled to correlate the alterations in substrate affinity with the different amino acid substitutions. Conclusions: We demonstrated the key role of Y295C mutation in HMF reduction by Adh1p. We generated and kinetically characterized a group of protein variants using two furaldehyde compounds of industrial relevance. Also, we showed that there is a threshold after which higher in vitro HMF reduction activities do not correlate any more with faster in vivo rates of HMF conversion, indicating other cell limitations in the conversion of HMF.
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39.
  • Laadan, Boaz, et al. (författare)
  • Identification of an NADH-dependent 5-hydroxymethylfurfural-reducing alcohol dehydrogenase in Saccharomyces cerevisiae.
  • 2008
  • Ingår i: Yeast. - : Wiley. - 1097-0061 .- 0749-503X. ; 25:3, s. 191-198
  • Tidskriftsartikel (refereegranskat)abstract
    • We report on the identification and characterization of a mutated alcohol dehydrogenase 1 from the industrial Saccharomyces cerevisiae strain TMB3000 that mediates the NADH-dependent reduction of 5-hydroxymethylfurfural (HMF) to 2,5-bis-hydroxymethylfuran. The co-factor preference distinguished this alcohol dehydrogenase from the previously reported NADPH-dependent S. cerevisiae HMF alcohol dehydrogenase Adh6. The amino acid sequence revealed three novel mutations (S109P, L116S and Y294C) that were all predicted at the vicinity of the substrate binding site, which could explain the unusual substrate specificity. Increased biomass production and HMF conversion rate were achieved in a CEN.PK S. cerevisiae strain overexpressing the mutated ADH1 gene. Copyright (c) 2008 John Wiley & Sons, Ltd.
  •  
40.
  • Lahiri, SD, et al. (författare)
  • Crystallization and preliminary X-ray diffraction studies of beta-phosphoglucomutase from Lactococcus lactus
  • 2002
  • Ingår i: Acta Crystallographica. Section D: Biological Crystallography. - 1399-0047. ; 58, s. 324-326
  • Tidskriftsartikel (refereegranskat)abstract
    • beta-Phosphoglucomutase (beta-PGM), a 28 kDa monomer, catalyzes the reversible conversion of beta-D-glucose-1-phosphate to beta-D-glucose-6-phosphate in maltose metabolism in a variety of organisms. Sequence analysis of beta-PGM indicates that it is a member of the haloacid dehalogenase (HAD) enzyme superfamily, which evolved to cleave C-Cl, C-P and C-OP bonds in a variety of substrates. beta-PGM has been crystallized using the hanging-drop method. Diffraction-quality crystals of the native protein have been obtained from two conditions, both belonging to space group P2(1)2(1)2(1), with unit-cell parameters a = 53.67, b = 92.78, c = 111.60 and a = 53.21, b = 57.01, c = 76.11 Angstrom. To solve the phase problem, selenomethionine (SeMet) containing alpha-PGM crystals have been grown. The SeMet-containing crystals diffract to high resolution only when grown by microseeding with native crystals. A three-wavelength data set has been collected to 2.3 Angstrom on crystals of the SeMet-substituted beta-PGM. The structure solution is currently being attempted by the multi-wavelength anomalous diffraction (MAD) phasing method.
  •  
41.
  • Lantz, Pär-Gunnar, et al. (författare)
  • Use of aqueous two-phase systems in sample preparation for polymerase chain reaction-based detection of microorganisms
  • 1996
  • Ingår i: Journal of Chromatography. B. - : Elsevier BV. - 1572-6495. ; 680:1-2, s. 165-170
  • Tidskriftsartikel (refereegranskat)abstract
    • An aqueous two-phase system, consisting of poly(ethylene glycol) (PEG) and dextran, was employed to separate polymerase chain reaction (PCR)-inhibitory substances from bacterial cells. The PCR inhibition of four soft cheeses was examined and three of them were found to be strongly PCR-inhibitory. Extraction of the PCR-inhibitory soft cheeses inoculated with Listeria monocytogenes in an aqueous two-phase system containing 8% (w/w) PEG 4000 and 8% (w/w) dextran 500, was found to lower the PCR detection level of L. monocytogenes by more than four orders of magnitude in two of the cheeses compared to the case where no such sample pretreatment was performed. Depending on the type of cheese used, the PCR-inhibitory factors were found to be enriched in either the top or bottom phase in the aqueous two-phase system. These results show that different soft cheeses contain different types and amounts of PCR-inhibitory substances.
  •  
42.
  • Levander, Fredrik, et al. (författare)
  • Enhanced Exopolysaccharide Production by Metabolic Engineering of Streptococcus thermophilus.
  • 2002
  • Ingår i: Applied and Environmental Microbiology. - 0099-2240. ; 68:2, s. 784-790
  • Tidskriftsartikel (refereegranskat)abstract
    • It is possible that the low levels of production of exopolysaccharides (EPSs) by lactic acid bacteria could be improved by altering the levels of enzymes in the central metabolism that influence the production of precursor nucleotide sugars. To test this hypothesis, we identified and cloned the galU gene, which codes for UDP glucose pyrophosphorylase (GalU) in Streptococcus thermophilus LY03. Homologous overexpression of the gene led to a 10-fold increase in GalU activity but did not have any effect on the EPS yield when lactose was the carbon source. However, when galU was overexpressed in combination with pgmA, which encodes phosphoglucomutase (PGM), the EPS yield increased from 0.17 to 0.31 g/mol of carbon from lactose. A galactose-fermenting LY03 mutant (Gal(+)) with increased activities of the Leloir enzymes was also found to have a higher EPS yield (0.24 g/mol of carbon) than the parent strain. The EPS yield was further improved to 0.27 g/mol of carbon by overexpressing galU in this strain. However, the highest EPS yield, 0.36 g/mol of carbon, was obtained when pgmA was knocked out in the Gal(+) strain. Measurements of the levels of intracellular metabolites in the cultures revealed that the Gal(+) strains had considerably higher glucose 1-phosphate levels than the other strains, and the strain lacking PGM activity had threefold-higher levels of glucose 1-phosphate than the other Gal(+) strains. These results show that it is possible to increase EPS production by altering the levels of enzymes in the central carbohydrate metabolism.
  •  
43.
  • Lübeck, P S, et al. (författare)
  • Towards an international standard for PCR-based detection of food-borne thermotolerant Campylobacters: assay development and analytical validation.
  • 2003
  • Ingår i: Applied and Environmental Microbiology. - 0099-2240. ; 69:9, s. 5664-5669
  • Tidskriftsartikel (refereegranskat)abstract
    • As part of a European research project (FOOD-PCR), we developed a standardized and robust PCR detection assay specific for the three most frequently reported food-borne pathogenic Campylobacter species, C. jejuni, C. coli, and C. lari. Fifteen published and unpublished PCR primers targeting the 16S rRNA gene were tested in all possible pairwise combinations, as well as two published primers targeting the 23S rRNA gene. A panel of 150 strains including target and nontarget strains was used in an in-house validation. Only one primer pair, OT1559 plus 18-1, was found to be selective. The inclusivity and exclusivity were 100 and 97%, respectively. In an attempt to find a thermostable DNA polymerase more resistant than Taq to PCR inhibitors present in chicken samples, three DNA polymerases were evaluated. The DNA polymerase Tth was not inhibited at a concentration of 2% (vol/vol) chicken carcass rinse, unlike both Taq DNA polymerase and DyNAzyme. Based on these results, Tth was selected as the most suitable enzyme for the assay. The standardized PCR test described shows potential for use in large-scale screening programs for food-borne Campylobacter species under the assay conditions specified.
  •  
44.
  • Luhrig, Katharina, et al. (författare)
  • Bacterial Community Analysis of Drinking Water Biofilms in Southern Sweden
  • 2015
  • Ingår i: Microbes and Environments. - 1342-6311. ; 30:1, s. 99-107
  • Tidskriftsartikel (refereegranskat)abstract
    • Next-generation sequencing of the V1-V2 and V3 variable regions of the 16S rRNA gene generated a total of 674,116 reads that described six distinct bacterial biofilm communities from both water meters and pipes. A high degree of reproducibility was demonstrated for the experimental and analytical work-flow by analyzing the communities present in parallel water meters, the rare occurrence of biological replicates within a working drinking water distribution system. The communities observed in water meters from households that did not complain about their drinking water were defined by sequences representing Proteobacteria (82-87%), with 22-40% of all sequences being classified as Sphingomonadaceae. However, a water meter biofilm community from a household with consumer reports of red water and flowing water containing elevated levels of iron and manganese had fewer sequences representing Proteobacteria (44%); only 0.6% of all sequences were classified as Sphingomonadaceae; and, in contrast to the other water meter communities, markedly more sequences represented Nitrospira and Pedomicrobium. The biofilm communities in pipes were distinct from those in water meters, and contained sequences that were identified as Mycobacterium, Nocardia, Desulfovibrio, and Sulfuricurvum. The approach employed in the present study resolved the bacterial diversity present in these biofilm communities as well as the differences that occurred in biofilms within a single distribution system, and suggests that next-generation sequencing of 16S rRNA amplicons can show changes in bacterial biofilm communities associated with different water qualities.
  •  
45.
  • Löfström, Charlotta, et al. (författare)
  • Culture-independent quantification of Salmonella enterica in carcass gauze swabs by flotation prior to real-time PCR
  • 2011
  • Ingår i: International Journal of Food Microbiology. - : Elsevier BV. - 0168-1605 .- 1879-3460. ; 145:SUPPL. 1, s. S103-S109
  • Tidskriftsartikel (refereegranskat)abstract
    • To facilitate quantitative risk assessment in the meat production chain, there is a need for culture-independent quantification methods. The aim of this study was to evaluate the use of flotation, a non-destructive sample preparation method based on traditional buoyant density centrifugation, for culture-independent quantification of intact Salmonella in pig carcass gauze swabs (100cm2) prior to quantitative PCR (qPCR). A novel approach was investigated, excluding the homogenization step prior to flotation, to improve the detection limit and speed up the quantification procedure. The buoyant density of two Salmonella strains in different growth conditions was determined to be 1.065-1.092g/ml. Based on these data, an optimal discontinuous flotation with three different density layers, ~1.200, 1.102 and 1.055g/ml, was designed for extracting intact Salmonella cells from pig carcass swabs. The method allowed accurate quantification from 4.4×102 to at least 2.2×107CFU Salmonella per swab sample using qPCR (without preceding DNA extraction) or selective plating on xylose lysine deoxycholate agar. Samples with 50CFU could be detected occasionally but fell outside the linear range of the standard curve. The swab samples showed a broad biological diversity; for seven samples not inoculated with Salmonella, the microbial background flora (BGF) was determined to 5.0±2.2 log CFU/ml sample withdrawn after flotation. It was determined that the proceeding PCR step was inhibited by BGF concentrations of ≥6.1×108CFU/swab sample, but not by concentrations ≤6.1×106CFU/swab sample. By using the gauze swabs directly in the flotation procedure, the homogenization step normally used for preparation of food-related samples could be excluded, which simplified the culture-independent quantification method considerably. © 2010 Elsevier B.V.
  •  
46.
  • Löfström, Charlotta, et al. (författare)
  • Improvement and validation of RAPD in combination with PFGE analysis of Salmonella enterica ssp enterica serovar Senftenberg strains isolated from feed mills
  • 2006
  • Ingår i: Veterinary Microbiology. - : Elsevier BV. - 0378-1135 .- 1873-2542. ; 114:3-4, s. 345-351
  • Tidskriftsartikel (refereegranskat)abstract
    • In 1995 and 1996 a Swedish feed mill had problems due to a persistent contamination of Salmonella enterica spp. enterica serovar Senftenberg that was difficult to eliminate. Forty-eight strains isolated from the feed mill, together with unrelated strains included to evaluate the discriminatory power and reproducibility, were analysed by pulsed-field gel electrophoresis (PFGE). The source of contamination in the feed mill was identified and preventative measures were taken, that led to a resolution of the problem. A previously developed randomly amplified polymorphic DNA (RAPD) protocol was used, to evaluate a rapid and low-cost alternative to PFGE typing. The use of the alternative thermostable DNA polymerase Tth was shown to increase the reproducibility of the RAPD analysis. The reproducibility, in terms of Pearson's and Dice's similarity coefficients for duplicate runs, increased from 72.0 +/- 16.9% and 72.3 +/- 12.9% for Taq to 91.6 +/- 7.5% and 90.9 +/- 5.3% for the fingerprints obtained for the RAPD method employing Tth DNA polymerase. Simpson's index of diversity was calculated and found to be 0.580 for RAPD and 0.896 for PFGE. All of the seven RAPD, types could be subdivided into one or more PFGE types, whereas none of the 22 PFGE types was divided into more than one RAPD type. RAPD provides a simple, rapid and powerful screening method that can be used to initially select isolates for further analysis by PFGE
  •  
47.
  • Löfström, Charlotta, et al. (författare)
  • Rapid and Specific Detection of Salmonella spp. in Animal Feed Samples by PCR after Culture Enrichment
  • 2004
  • Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 70:1, s. 69-75
  • Tidskriftsartikel (refereegranskat)abstract
    • A PCR procedure has been developed for routine analysis of viable Salmonella spp. in feed samples. The objective was to develop a simple PCR-compatible enrichment procedure to enable DNA amplification without any sample pretreatment such as DNA extraction or cell lysis. PCR inhibition by 14 different feed samples and natural background flora was circumvented by the use of the DNA polymerase Tth. This DNA polymerase was found to exhibit a high level of resistance to PCR inhibitors present in these feed samples compared to DyNAzyme II, FastStart Taq, Platinum Taq, Pwo, rTth, Taq, and Tfl. The specificity of the Tth assay was confirmed by testing 101 Salmonella and 43 non-Salmonella strains isolated from feed and food samples. A sample preparation method based on culture enrichment in buffered peptone water and DNA amplification with Tth DNA polymerase was developed. The probability of detecting small numbers of salmonellae in feed, in the presence of natural background flora, was accurately determined and found to follow a logistic regression model. From this model, the probability of detecting 1 CFU per 25 g of feed in artificially contaminated soy samples was calculated and found to be 0.81. The PCR protocol was evaluated on 155 naturally contaminated feed samples and compared to an established culture-based method, NMKL-71. Eight percent of the samples were positive by PCR, compared with 3% with the conventional method. The reasons for the differences in sensitivity are discussed. Use of this method in the routine analysis of animal feed samples would improve safety in the food chain.
  •  
48.
  • Löfström, Charlotta, et al. (författare)
  • Validation of a Diagnostic PCR Method for Routine Analysis of Salmonella spp. in Animal Feed Samples
  • 2008
  • Ingår i: Food Analytical Methods. - : Springer Science and Business Media LLC. - 1936-9751 .- 1936-976X. ; 1:1, s. 23-27
  • Tidskriftsartikel (refereegranskat)abstract
    • As a part of a validation study, a comparative study of a PCR method and the standard culture-based method NMKL-71, for detection of Salmonella, was performed according to the validation protocol from the Nordic validation organ for validation of alternative microbiological methods (NordVal) on 250 artificially or naturally contaminated animal feed samples. The PCR method is based on culture enrichment in buffered peptone water followed by PCR using the DNA polymerase Tth and an internal amplification control. No significant difference was found between the two methods. The relative accuracy, relative sensitivity and relative specificity were found to be 96.0, 97.3, and 98.8%, respectively. PCR inhibition was observed for rape seed samples. For the acidified feed samples, more Salmonella-positive samples were found with the PCR method compared to the NMKL method. This study focuses on the growing demand for validated diagnostic PCR methods for routine analysis of animal feed and food samples to assure safety in the food production chain.
  •  
49.
  • Lövenklev, Maria, et al. (författare)
  • Quantitative interaction effects of carbon dioxide, sodium chloride, and sodium nitrite on neurotoxin gene expression in nonproteolytic Clostridium botulinum type B
  • 2004
  • Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 70:5, s. 2928-2934
  • Tidskriftsartikel (refereegranskat)abstract
    • The effects of carbon dioxide, sodium chloride, and sodium nitrite on type B botulinum neurotoxin (BoNT/B) gene (cntB) expression in nonproteolytic Clostridium botulinum were investigated in a tryptone-peptone-yeast extract (TPY) medium. Various concentrations of these selected food preservatives were studied by using a complete factorial design in order to quantitatively study interaction effects, as well as main effects, on the following responses: lag phase duration (LPD), growth rate, relative cntB expression, and extracellular BoNT/B production. Multiple linear regression was used to set up six statistical models to quantify and predict these responses. All combinations of NaCl and NaNO2 in the growth medium resulted in a prolonged lag phase duration and in a reduction in the specific growth rate. In contrast, the relative BoNT/B gene expression was unchanged, as determined by the cntB-specific quantitative reverse transcription-PCR method. This was confirmed when we measured the extracellular BoNT/B concentration by an enzyme-linked immunosorbent assay. CO2 was found to have a major effect on gene expression when the cntB mRNA levels were monitored in the mid-exponential, late exponential, and late stationary growth phases. The expression of cntB relative to the expression of the 16S rRNA gene was stimulated by an elevated CO2 concentration; the cntB mRNA level was fivefold greater in a 70% CO2 atmosphere than in a 10% CO2 atmosphere. These findings were also confirmed when we analyzed the extracellular BoNT/B concentration; we found that the concentrations were 27 ng·ml -1·unit of optical density-1 in the 10% CO 2 atmosphere and 126 ng·ml-1·unit of optical density-1 in the 70% CO2 atmosphere.
  •  
50.
  • Lövenklev, Maria, et al. (författare)
  • Relative neurotoxin gene expression in Clostridium botulinum type B, determined using quantitative reverse transcription-PCR
  • 2004
  • Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 70:5, s. 2919-2927
  • Tidskriftsartikel (refereegranskat)abstract
    • A quantitative reverse transcription-PCR (qRT-PCR) method was developed to monitor the relative expression of the type B botulinum neurotoxin (BoNT/B) gene (cntB) in Clostridium botulinum. The levels of cntB mRNA in five type B strains were accurately monitored by using primers specific for cntB and for the reference gene encoding the 16S rRNA. The patterns and relative expression of cntB were different in the different strains. Except for one of the strains investigated, an increase in cntB expression was observed when the bacteria entered the early stationary growth phase. In the proteolytic strain C. botulinum ATCC 7949, the level of cntB mRNA was four- to fivefold higher than the corresponding levels in the other strains. This was confirmed when we quantified the production of extracellular BoNT/B by an enzyme-linked immunosorbent assay and measured the toxicity of BoNT/B by a mouse bioassay. When the effect of exposure to air on cntB expression was investigated, no decline in the relative expression was observed in spite of an 83% reduction in the viable count based on the initial cell number. Instead, the level of cntB mRNA remained the same. When there was an increase in the sodium nitrite concentration, the bacteria needed a longer adjustment time in the medium before exponential growth occurred. In addition, there was a reduction in the expression of cntB compared to the expression of the 16S rRNA gene at higher sodium nitrite concentrations. This was most obvious in the late exponential growth phase, but at the highest sodium nitrite concentration investigated, 45 ppm, a one- to threefold decline in the cntB mRNA level was observed in all growth phases.
  •  
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