Research Topics
Genomes and Genes | K RudiSummaryAffiliation: Norwegian Food Research Institute Country: Norway Publications
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Publications
Nested evolution of a tRNA(Leu)(UAA) group I intron by both horizontal intron transfer and recombination of the entire tRNA locusKnut Rudi
MATFORSK, Norwegian Food Research Institute, 1430 As, Norway
J Bacteriol 184:666-71. 2002..e., wherein the intron has been transferred horizontally (probably through a single or a few events) to a tRNA(Leu)(UAA) gene which is located within a unstable genome region...
Rapid identification and classification of bacteria by 16S rDNA restriction fragment melting curve analyses (RFMCA)Knut Rudi
MATFORSK Norwegian Food Research Institute, Oslo, Norway
Food Microbiol 24:474-81. 2007....- A novel multiplex quantitative DNA array based PCR (MQDA-PCR) for quantification of transgenic maize in food and feedKnut Rudi
MATFORSK, Norwegian Food Research Institute, Osloveien 1, N 1430 Aas, Norway
Nucleic Acids Res 31:e62. 2003..The samples could, by both methods, be quantified as containing >2%, between 1 and 2%, between 0.1 and 1%, or <0.1% in 43 out of 47 determinations. The described method is modular, and thus suited for future needs in GM detection... - Protocols for 16S rDNA array analyses of microbial communities by sequence-specific labeling of DNA probesKnut Rudi
MATFORSK Norwegian Food Research Institute, As, Norway
ScientificWorldJournal 3:578-84. 2003..Protocols are presented for DNA purification, probe construction, probe labeling, and DNA array hybridizations... - Comparison of membranes and glass slides for 16S rDNA array analyses of microbial communities by sequence-specific labeling of DNA probesKnut Rudi
MATFORSK, Norwegian Food Research Institute, Osloveien, As, Norway
Prep Biochem Biotechnol 33:197-208. 2003..The advantage of the glass slides is that multiple fluorescence colors can be detected simultaneously, and that internal controls can be used for normalization. This approach is also suited for high throughput screenings... - Alignment-independent bilinear multivariate modelling (AIBIMM) for global analyses of 16S rRNA gene phylogenyKnut Rudi
MATFORSK Norwegian Food Research Institute, Osloveien 1, 1430 As, Norway
Int J Syst Evol Microbiol 56:1565-75. 2006..We conclude that AIBIMM represents a novel phylogenetic framework suitable for accommodating the current exponential growth of 16S rRNA gene sequences in the public domain... - Real-time closed tube single nucleotide polymorphism (SNP) quantification in pooled samples by quencher extension (QEXT)Knut Rudi
MATFORSK Norwegian Food Research Institute, Osloveien 1, 1430 As, Norway
Nucleic Acids Res 31:e117. 2003..05). The QEXT method is directly adaptable to current real-time PCR equipment and is thus suited for high throughput and a wide application range... - Direct real-time PCR quantification of Campylobacter jejuni in chicken fecal and cecal samples by integrated cell concentration and DNA purificationKnut Rudi
MATFORSK, Norwegian Food Research Institute, 1430 As, Norway
Appl Environ Microbiol 70:790-7. 2004..Understanding the colonization kinetics in poultry is therefore of great importance for controlling human infections by this bacterium... - Explorative multivariate analyses of 16S rRNA gene data from microbial communities in modified-atmosphere-packed salmon and coalfishKnut Rudi
MATFORSK Norwegian Food Research Institute, Osloveien 1, 1430 As, Norway
Appl Environ Microbiol 70:5010-8. 2004..Such information is crucial in controlled food production when, for example, the hazard analysis of critical control points principle is used... - Multiplex real-time single nucleotide polymorphism detection and quantification by quencher extensionKnut Rudi
MATFORSK Norwegian Food Research Institute, As, Norway
Biotechniques 40:323-9. 2006..With the emergence of new fluorochromes with narrow emission spectra, we foresee great potential for increasing the multiplex level in the future... - Use of ethidium monoazide and PCR in combination for quantification of viable and dead cells in complex samplesKnut Rudi
MATFORSK, Norwegian Institute for Food Research, Osloveien 1, 1430 As, Norway
Appl Environ Microbiol 71:1018-24. 2005..In conclusion, EMA-PCR offers a novel real-time PCR method for quantitative distinction between viable and dead cells with potentially very wide application... - Detection of viable and dead Listeria monocytogenes on gouda-like cheeses by real-time PCRK Rudi
MATFORSK, Norwegian Food Research Institute, Osloveien, As, Norway
Lett Appl Microbiol 40:301-6. 2005..The aim of this work was to develop novel real-time PCR diagnostics to detect the presence of viable, dead or viable but not culturable (VBNC) cells on gouda-like cheeses... - Explorative screening of complex microbial communities by real-time 16S rDNA restriction fragment melting curve analysesKnut Rudi
MATFORSK Norwegian Food Research Institute, As, Norway
Biotechniques 39:116-21. 2005..Our conclusions are that RFMCA is robust, gives a relatively high resolution, and has the potential for high-throughput explorative screenings of microbial communities and large clone libraries... - Multi locus fingerprinting of Listeria monocytogenes by sequence-specific labeling of DNA probes combined with array hybridizationKnut Rudi
MATFORSK, Norwegian Food Research Institute, Osloveien 1, N 1430 As, Norway
FEMS Microbiol Lett 220:9-14. 2003..This comparison showed that our DNA array method gave good discrimination between the strains analyzed. In conclusion, the DNA array-based MLST method is a promising tool for fingerprint bacteria... - Use of multivariate statistics for 16S rRNA gene analysis of microbial communitiesK Rudi
MATFORSK Norwegian Food Research Institute, Osloveien 1, NO 1430 As, Norway
Int J Food Microbiol 120:95-9. 2007..We are currently investigating approaches to describe dynamic microbial community interactions. Our ultimate goal is to understand and model the main dynamic interactions in complete microbial communities... - Restriction cutting independent method for cloning genomic DNA segments outside the boundaries of known sequencesK Rudi
University of Oslo, Norway
Biotechniques 27:1170-2, 1176-7. 1999..The method was used to clone both the upstream (5') and the downstream (3') genomic regions of an intron-interrupted tRNA(Leu)(UAA) gene from three cyanobacteria belonging to the genus Microcystis... - Application of sequence-specific labeled 16S rRNA gene oligonucleotide probes for genetic profiling of cyanobacterial abundance and diversity by array hybridizationK Rudi
Division of General Genetics, Department of Biology, University of Oslo, 0315 Oslo, Norway
Appl Environ Microbiol 66:4004-11. 2000..The conclusions from these comparisons are that the genetic abundance profiles may provide a foundation for separating and quantifying genetically distinct groups of cyanobacteria in their natural habitats... - 16S rDNA analyses of the cyanobacterial microbiota through the water-column in a boreal lake with a metalimnic Planktothrix populationKnut Rudi
MATFORSK Norwegian Food Research Institute, As, Norway
Prep Biochem Biotechnol 35:301-12. 2005..Such approaches will be important in better understanding cyanobacterial microbiota and bloom dynamics... - Development and evaluation of a 16S ribosomal DNA array-based approach for describing complex microbial communities in ready-to-eat vegetable salads packed in a modified atmosphereKnut Rudi
MATFORSK, Norwegian Food Research Institute, Osloveien 1, N 1430 As, Norway
Appl Environ Microbiol 68:1146-56. 2002..The practical implications of these results are that microbial communities in ready-to-eat vegetable salads can be diverse and that microbial composition is dependent both on the origin of the raw material and on the storage conditions... - Development and application of new nucleic acid-based technologies for microbial community analyses in foodsKnut Rudi
MATFORSK, Norwegian Food Research Institute, As
Int J Food Microbiol 78:171-80. 2002.... - Internal controls for normalizing DNA arraysK Rudi
MATFORSK, Norwegian Food Research Institute, As
Biotechniques 33:496, 498, 500 passim. 2002 - Subtyping Listeria monocytogenes through the combined analyses of genotype and expression of the hlyA virulence determinantK Rudi
MATFORSK, Norwegian Food Research Institute, As, Norway
J Appl Microbiol 94:720-32. 2003..The aim of this work was to obtain a better subtyping of L. monocytogenes through utilization of combined analyses of genotype and the expression of the virulence determinant hlyA... - Application of 5'-nuclease PCR for quantitative detection of Listeria monocytogenes in pure cultures, water, skim milk, and unpasteurized whole milkH K Nogva
MATFORSK, Norwegian Food Research Institute, N 1430 As, Norway
Appl Environ Microbiol 66:4266-71. 2000..In conclusion, a complete quantitative method for L. monocytogenes in water and in skimmed and raw milk was developed... - Abrupt temporal fluctuations in the chicken fecal microbiota are explained by its gastrointestinal originM Sekelja
Nofima Mat, The Norwegian Institute of Food, Fisheries and Aquaculture Research, As, Norway
Appl Environ Microbiol 78:2941-8. 2012..This knowledge will be important for future understanding of factors affecting shedding of both harmful and beneficial gastrointestinal bacteria through feces... 
Novel 16S rRNA gene analyses reveal new in vitro effects of insoluble barley fibres on the human faecal microbiotaK Rudi
Matforsk AS, Nofima Food, Osloveien, Norway
Lett Appl Microbiol 48:433-9. 2009..A major reason for the limited knowledge is that there are currently no proper tools to analyse the complete GI microbiota...- Multivariate analysis of complex DNA sequence electropherograms for high-throughput quantitative analysis of mixed microbial populationsPål Trosvik
Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, Oslo, Norway
Appl Environ Microbiol 73:4975-83. 2007..The method presented here is, however, applicable to any experimental scenario where the interest is quantification of GCUs in genetically heterogeneous DNA samples... - Detection of toxin-producing cyanobacteria by use of paramagnetic beads for cell concentration and DNA purificationK Rudi
Department of Biology, University of Oslo, Norway
Appl Environ Microbiol 64:34-7. 1998..The detection limits and the simplicity of the method (paramagnetic beads can be handled in automated systems) suggest that our method is suitable for routine environmental monitoring... - Evolution of cyanobacteria by exchange of genetic material among phyletically related strainsK Rudi
Department of Biology, University of Oslo, Norway
J Bacteriol 180:3453-61. 1998..We also suggest that exchange of genetic material for neutrally evolving genes may explain the apparent stability of cyanobacterial morphological characters, perhaps over billions of years... - Cyanobacterial tRNA(Leu)(UAA) group I introns have polyphyletic originK Rudi
Department of Biology, University of Oslo, Norway
FEMS Microbiol Lett 156:293-8. 1997..Our sequence comparison and phyletic reconstruction suggest lateral transfer of the intron (possibly trough mobility), and a polyphyletic origin of cyanobacterial tRNA(Leu)(UAA) group I introns... - Prevention of intestinal Campylobacter jejuni colonization in broilers by combinations of in-feed organic acidsB Skånseng
Nofima Mat, As, Norway
J Appl Microbiol 109:1265-73. 2010..We have tested the effect of various combinations of formic acid and sorbate on Campylobacter jejuni colonization in broiler chickens to reduce the colonization of this zoonotic pathogen in broiler chicken flocks... - Quantification of toxic cyanobacteria in water by use of competitive PCR followed by sequence-specific labeling of oligonucleotide probesK Rudi
Department of Biology, University of Oslo, Norway
Appl Environ Microbiol 64:2639-43. 1998..This approach can easily be adapted to a wide range of bacterial species and has the potential for simultaneous detection and quantitation of several different target organisms by a single assay... - Discriminatory power, typability, and accuracy of single nucleotide extension microarraysIngunn Berget
MATFORSK, Oslovn 1, 1430 As, Norway and Cigene, Norwegian University of Life Sciences UMB, 1430, As, Norway
J AOAC Int 90:802-9. 2007..The classification error for our experimental data was 3.2% (after removing 5 high error SNPs). We therefore conclude that SNE microarrays are promising for future high-throughput typing of bacteria... - Natural variation in the microcystin synthetase operon mcyABC and impact on microcystin production in Microcystis strainsBjørg Mikalsen
Department of Biology, University of Oslo, Norway
J Bacteriol 185:2774-85. 2003..Collectively, these results suggest that recombination between imperfect repeats, gene loss, and horizontal gene transfer can explain the distribution and variation within the mcyABC operon... - Convergent temporal dynamics of the human infant gut microbiotaPål Trosvik
Nofima Mat, Norwegian Food Research Institute, As, Norway
ISME J 4:151-8. 2010..Considering the predictive ability and convergence of our phylum-level model, we now propose that deterministic bacterial-bacterial interactions are more important for shaping the human infant gut microbiota than previously anticipated... - Comparison of chicken gut colonisation by the pathogens Campylobacter jejuni and Clostridium perfringens by real-time quantitative PCRBeate Skånseng
MATFORSK, Norwegian Food Research Institute, Osloveien 1, N 1430 As, Norway
Mol Cell Probes 20:269-79. 2006..As demonstrated here, the development of new tools for high-throughput analyses will be of key importance for these studies... - Quencher extension for single nucleotide polymorphism quantification in bacterial typing and microbial community analysesKnut Rudi
Matforsk AS, Norwegian Food Research Institute, Oslo, Norway
Methods Mol Biol 345:111-7. 2006..The quencher extension protocol presented was developed for SNP allele quantification in Listeria monocytogenes and for microbial community analyses... 
Co-infection dynamics of a major food-borne zoonotic pathogen in chickenBeate Skånseng
MATFORSK, Norwegian Food Research Institute, As, Norway
PLoS Pathog 3:e175. 2007..This model represents a new understanding of C. jejuni epidemiology, with future implications for the development of novel intervention strategies...- Quality changes during refrigerated storage of MA-packaged pre-rigor fillets of farmed Atlantic cod (Gadus morhua L.) using traditional MAP, CO2 emitter, and vacuumA A Hansen
Matforsk AS, Norwegian Food Research Inst, N 1430 As, Norway
J Food Sci 72:M423-30. 2007..In MA packages with high O2 levels the Photobacterium was inhibited. It is concluded that CO2 emitters are well suited for reduction of transport volume for MA-packaged farmed cod... - Global responses of Escherichia coli to adverse conditions determined by microarrays and FT-IR spectroscopyBirgitte Moen
Nofima Mat, N 1430 As, Norway
Can J Microbiol 55:714-28. 2009..coli, underlining the importance of multiple strategies to begin to understand the effect on the whole cell... - Analysis of covariance patterns in gene expression data and FT-IR spectraAstrid Oust
Matforsk AS, Norwegian Food Research Institute, Osloveien 1, As, Norway
J Microbiol Methods 65:573-84. 2006..It was also shown that the use of FT-IR spectroscopy provided important information about the stress responses in the bacteria, information that was not detected from the DNA microarray data... - Biofilm formation and the presence of the intercellular adhesion locus ica among staphylococci from food and food processing environmentsTrond Møretrø
MATFORSK, Norwegian Food Research Institute, N 1430 As, Norway
Appl Environ Microbiol 69:5648-55. 2003..Biofilm formation on polystyrene was positively correlated with biofilm formation on stainless steel and with resistance to quaternary ammonium compounds, a group of disinfectants... - Potential influence of the first PCR cycles in real-time comparative gene quantificationsHege Karin Nogva
Norwegian Food Research Institute, As, Norway
Biotechniques 37:246-8, 250-3. 2004..Future applications of real-time PCR quantifications should account for the effect of the first few PCR cycles on the conclusions drawn... - Explorative multifactor approach for investigating global survival mechanisms of Campylobacter jejuni under environmental conditionsBirgitte Moen
Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Norway
Appl Environ Microbiol 71:2086-94. 2005..Basic knowledge about the survival mechanisms is of fundamental importance in preventing transmission of this bacterium through the food chain... - Characterizing mixed microbial population dynamics using time-series analysisPål Trosvik
Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
ISME J 2:707-15. 2008.... - Reduced spread of Campylobacter jejuni in broiler chickens by stimulating the bird's natural barriersB Moen
Nofima Norwegian Institute of Food, Fisheries and Aquaculture Research, As, Norway
J Appl Microbiol 113:1176-83. 2012..We have tested the effect of feed structure and feeding regime to prevent the spread of the zoonotic pathogen Campylobacter jejuni in broiler chicken flocks... - Ethidium monoazide for DNA-based differentiation of viable and dead bacteria by 5'-nuclease PCRHege Karin Nogva
Norwegian Food Research Institute, As, Norway
Biotechniques 34:804-8, 810, 812-3. 2003..In conclusion, the EMA method is promising for DNA-based differentiation between viable and dead bacteria... - Overview of DNA purification for nucleic acid-based diagnostics from environmental and clinical samplesKnut Rudi
Matforsk AS, Norwegian Food Research Institute, Oslo, Norway
Methods Mol Biol 345:23-35. 2006..This chapter will focus on the advantages and the disadvantages of the methods available... - Estimation of metagenome size and structure in an experimental soil microbiota from low coverage next-generation sequence dataT Frisli
Hedmark University College, Hamar, Norway
J Appl Microbiol 114:141-51. 2013..Here, we present a novel approach to estimate the size of all combined genomes for low coverage next-generation sequencing (NGS) data through empirically determined copy numbers of random DNA fragments... - Quality changes of prerigor filleted Atlantic salmon (Salmo salar L.) packaged in modified atmosphere using CO2 emitter, traditional MAP, and vacuumAnlaug Adland Hansen
Nofima Mat AS, Osloveien 1, N 1430 As, Norway
J Food Sci 74:M242-9. 2009..MA packaging with a CO(2) emitter and reduced g/p ratio gave similar or better results compared with traditional MAP, thus CO(2) emitters are well suited for reduction of volume of MA packaged farmed salmon fillet pieces... - Adapted tolerance to benzalkonium chloride in Escherichia coli K-12 studied by transcriptome and proteome analysesErlend Bore
MATFORSK, Norwegian Food Research Institute, Osloveien 1, N 1430 As, Norway
Microbiology 153:935-46. 2007..The results revealed that BC treatment might result in superoxide stress in E. coli... - Alignment-independent comparisons of human gastrointestinal tract microbial communities in a multidimensional 16S rRNA gene evolutionary spaceKnut Rudi
Hedmark University College, Holsetgt 31, 2306 Hamar, Norway
Appl Environ Microbiol 73:2727-34. 2007..Our density distribution analysis is also very efficient with respect to computer operation time, meeting the future requirements of large-scale screenings to understand the diversity and dynamics of microbial communities... - A microbial diagnostic microarray technique for the sensitive detection and identification of pathogenic bacteria in a background of nonpathogensTanja Kostic
Department of Bioresources, ARC Seibersdorf Research GmbH, A 2444 Seibersdorf, Austria
Anal Biochem 360:244-54. 2007..Detection sensitivity in the range of 0.1% has been demonstrated, far below the 5% detection limit of traditional microbial diagnostic microarrays... - Use of DNA quantification to measure growth and autolysis of Lactococcus and Propionibacterium spp. in mixed populationsJanneke Treimo
Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N 1432 As, Norway
Appl Environ Microbiol 72:6174-82. 2006..We conclude that our DNA approach will be a valuable tool for use in future analyses and for understanding autolysis in mixed bacterial populations... - Differentiation of important and closely related cereal plant species (Poaceae) in food by hybridization to an oligonucleotide arraySissel Beate Rønning
Section of Food and Feed Microbiology, National Veterinary Institute, Ullevålsveien 68, P O Box 8156 Dep, 0033 Oslo, Norway
J Agric Food Chem 53:8874-80. 2005.... - Detection and quantification of Shiga toxin-encoding genes in sheep faeces by real-time PCRCamilla Sekse
Department of Food Safety and Infection Biology, Norwegian School of Veterinary Science, P O Box 8146 Dep, N 0033 Oslo, Norway
Mol Cell Probes 19:363-70. 2005..This quantitative stx(1) and stx(2) assay may be important in assessing whether sheep harbouring Shiga toxin-producing bacteria represent a potential hazard to human health... - Direct haplotype-specific DNA sequencingHeidi Rudi
Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, Norway
Prep Biochem Biotechnol 36:253-7. 2006..We conclude that the haplotype-specific sequencing is robust, and that the approach has a potentially very wide application range for any diploid organism...