Tom Kristensen

• Taiaroa, George; Samuelsen, Ørjan; Kristensen, Tom; Økstad, Ole Andreas & Heikal, Adam (2018). Complete Genome Sequence of Pseudomonas aeruginosa K34-7, a Carbapenem-Resistant Isolate of the High-Risk Sequence Type 233. Microbiology Resource Announcements (MRA). 7(4), p. 1–2. doi: 10.1128/MRA.00886-18. Full text in Research Archive Show summary

  Carbapenem-resistant Pseudomonas aeruginosa is defined as a “critical” priority pathogen for the development of new antibiotics. Here we report the complete genome sequence of an extensively drug-resistant, Verona integron-encoded metallo-β-lactamase-expressing isolate belonging to the high-risk sequence type 233.

• Heikal, Adam; Samuelsen, Ørjan; Kristensen, Tom & Økstad, Ole Andreas Løchen (2017). Complete genome sequence of a multidrug-resistant, blaNDM-1-expressing Klebsiella pneumoniae K66-45 clinical isolate from Norway. Microbiology Resource Announcements (MRA). 5:e00601(27), p. 1–2. doi: 10.1128/genomeA.00601-17. Full text in Research Archive
• Ekblad, Bie; Nissen-Meyer, Jon & Kristensen, Tom (2017). Whole-genome sequencing of mutants with increased resistance against the two-peptide bacteriocin plantaricin JK reveals a putative receptor and potential docking site. PLOS ONE. doi: 10.1371/journal.pone.0185279. Full text in Research Archive Show summary

  By whole-genome sequencing of resistant mutants, a putative receptor for plantaricin JK, a two-peptide bacteriocin produced by some Lactobacillus plantarum strains, was identified in Lactobacillus plantarum NCFB 965 and Weissella viridescens NCFB 1655. The receptors of the two species had 66% identical amino acid sequences and belong to the amino acid-polyamine-organocation (APC) transporter protein family. The resistant mutants contained point mutations in the protein-encoding gene resulting in either premature stop codons, leading to truncated versions of the protein, or single amino acid substitutions. The secondary structure of the W. viridescens protein was predicted to contain 12 transmembrane (TM) helices, a core structure shared by most members of the APC protein family. The single amino acid substitutions that resulted in resistant strains were located in a confined region of the protein that consists of TM helix 10, which is predicted to be part of an inner membrane pore, and an extracellular loop between TM helix 11 and 12. By use of template-based modeling a 3D structure model of the protein was obtained, which visualizes this mutational hotspot region and further strengthen the hypothesis that it represents a docking site for plantaricin JK.

• Krabberød, Anders Kristian; Orr, Russell; Bråte, Jon; Kristensen, Tom; Bjørklund, Kjell Rasmus & Shalchian-Tabrizi, Kamran (2017). Single cell transcriptomics, mega-phylogeny and the genetic basis of morphological innovations in Rhizaria. Molecular Biology and Evolution (MBE). ISSN 0737-4038. doi: 10.1093/molbev/msx075. Full text in Research Archive Show summary

  The innovation of the eukaryote cytoskeleton enabled phagocytosis, intracellular transport and cytokinesis, and is responsible for the diversity of eukaryotic morphologies. Still, the relationship between phenotypic innovations in the cytoskeleton and their underlying genotype is poorly understood. To explore the genetic mechanism of morphological evolution of the eukaryotic cytoskeleton we provide the first single cell transcriptomes from uncultured, free-living unicellular eukaryotes: the polycystine radiolarian Lithomelissa setosa (Nassellaria) and Sticholonche zanclea (Taxopodida). A phylogenomic approach using 255 genes finds Radiolaria and Foraminifera as separate monophyletic groups (together as Retaria), while Cercozoa is shown to be paraphyletic. Analysis of the genetic components of the cytoskeleton and mapping of the evolution of these to the revised phylogeny of Rhizaria reveal lineage-specific gene duplications and neofunctionalization of α and β tubulin in Retaria, actin in Retaria and Endomyxa, and Arp2/3 complex genes in Chlorarachniophyta. We show how genetic innovations have shaped cytoskeletal structures in Rhizaria, and how single cell transcriptomics can be applied for resolving deep phylogenies and studying gene evolution in uncultured protist species.

• Oppegård, Camilla; Kjos, Morten; Veening, Jan-Willem; Nissen-Meyer, Jon & Kristensen, Tom (2016). A putative amino acid transporter determines sensitivity to the two-peptide bacteriocin plantaricin JK. MicrobiologyOpen. doi: 10.1002/mbo3.363. Full text in Research Archive Show summary

  Lactobacillus plantarum produces a number of antimicrobial peptides (bacteriocins) that mostly target closely related bacteria. Although bacteriocins are important for the ecology of these bacteria, very little is known about how the peptides target sensitive cells. In this work, a putative membrane protein receptor of the two-peptide bacteriocin plantaricin JK was identified by comparing Illumina sequence reads from plantaricin JK-resistant mutants to a crude assembly of the sensitive wild-type Weissella viridescens genome using the polymorphism discovery tool VAAL. Ten resistant mutants harbored altogether seven independent mutations in a gene encoding an APC superfamily protein with 12 transmembrane helices. The APC superfamily transporter thus is likely to serve as a target for plantaricin JK on sensitive cells.

• Kjos, Morten; Oppegård, Camilla; Diep, Dzung Bao; Nes, Ingolf; Veening, Jan-Willem & Nissen-Meyer, Jon [Show all 7 contributors for this article] (2014). Sensitivity to the two-peptide bacteriocin lactococcin G is dependent on UppP, an enzyme involved in cell-wall synthesis. Molecular Microbiology. ISSN 0950-382X. 92(6), p. 1177–1187. doi: 10.1111/mmi.12632. Full text in Research Archive
• Sogge, Hanne; Rohrlack, Thomas; Rounge, Trine Ballestad; Sønstebø, Jørn Henrik; Tooming-Klunderud, Ave & Kristensen, Tom [Show all 7 contributors for this article] (2013). Gene flow, recombination, and selection in cyanobacteria: population structure of geographically related Planktothrix Freshwater Strains. Applied and Environmental Microbiology. ISSN 0099-2240. 79(2), p. 508–515. doi: 10.1128/AEM.02417-12. Full text in Research Archive Show summary

  Several Planktothrix strains, each producing a distinct oligopeptide profile, have been shown to coexist within Lake Steinsfjorden (Norway). Using nonribosomal peptide synthetase (NRPS) genes as markers, it has been shown that the Planktothrix community comprises distinct genetic variants displaying differences in bloom dynamics, suggesting a Planktothrix subpopulation structure. Here, we investigate the Planktothrix variants inhabiting four lakes in southeast of Norway utilizing both NRPS and non-NRPS genes. Phylogenetic analyses showed similar topologies for both NRPS and non-NRPS genes, and the lakes appear to have similar structuring of Planktothrix genetic variants. The structure of distinct variants was also supported by very low genetic diversity within variants compared to the between-variant diversity. Incongruent topologies and split decomposition revealed recombination events between Planktothrix variants. In several strains the gene variants seem to be a result of recombination. Both NRPS and non-NRPS genes are dominated by purifying selection; however, sites subjected to positive selection were also detected. The presence of similar and well-separated Planktothrix variants with low internal genetic diversity indicates gene flow within Planktothrix populations. Further, the low genetic diversity found between lakes (similar range as within lakes) indicates gene flow also between Planktothrix populations and suggests recent, or recurrent, dispersals. Our data also indicate that recombination has resulted in new genetic variants. Stability within variants and the development of new variants are likely to be influenced by selection patterns and within-variant homologous recombination.

• Uzelac, Gordana; Kojic, Milan; Lozo, Jelena; Aleksandrzak-Piekarczyk, Tamara; Gabrielsen, Christina & Kristensen, Tom [Show all 9 contributors for this article] (2013). A Zn-dependent metallopeptidase is responsible for sensitivity to LsbB, a class II leaderless bacteriocin of Lactococcus lactis subsp. lactis BGMN1-5. Journal of Bacteriology. ISSN 0021-9193. doi: 10.1128/JB.00859-13. Full text in Research Archive
• Håvelsrud, Othilde Else; Haverkamp, Thomas Hendricus Augustus; Kristensen, Tom; Jakobsen, Kjetill Sigurd & Rike, Anne Gunn Larsen (2013). Metagenomics in CO2 Monitoring. Energy Procedia. 37, p. 4215–4233. doi: 10.1016/j.egypro.2013.06.324. Full text in Research Archive Show summary

  Leakage from CO2 storage areas is likely to affect the microbial communities in the overlaying sediments. We have conducted a baseline characterization of the microbial communities present in the surface sediments overlaying the Johansen formation, a potential site for CO2 storage, using metagenomics. We detected six abundant potentially CO2 fixing strains (e.g. Nitrosopumilus maritimus SCM1) as well as key genes for CO2 fixation pathways (e.g. the reductive tricarboxylic acid cycle and the Wood Ljungdahl pathway). Assuming this fraction of the community would increase in case of CO2 leakage; this information could be used as part of a surveillance project.

• Håvelsrud, Othilde Else; Haverkamp, Thomas Hendricus Augustus; Kristensen, Tom; Jakobsen, Kjetill Sigurd & Rike, Anne Gunn Larsen (2012). Metagenomic and geochemical characterization of pockmarked sediments overlaying the Troll petroleum reservoir in the North Sea. BMC Microbiology. 12(203). doi: 10.1186/1471-2180-12-203. Full text in Research Archive Show summary

  Background Pockmarks (depressions in the seabed) have been discovered throughout the world’s oceans and are often related to hydrocarbon seepage. Although high concentrations of pockmarks are present in the seabed overlaying the Troll oil and gas reservoir in the northern North Sea, geological surveys have not detected hydrocarbon seepage in this area at the present time. In this study we have used metagenomics to characterize the prokaryotic communities inhabiting the surface sediments in the Troll area in relation to geochemical parameters, particularly related to hydrocarbon presence. We also investigated the possibility of increased potential for methane oxidation related to the pockmarks. Five metagenomes from pockmarks and plain seabed sediments were sequenced by pyrosequencing (Roche/454) technology. In addition, two metagenomes from seabed sediments geologically unlikely to be influenced by hydrocarbon seepage (the Oslofjord) were included. The taxonomic distribution and metabolic potential of the metagenomes were analyzed by multivariate analysis and statistical comparisons to reveal variation within and between the two sampling areas. Results The main difference identified between the two sampling areas was an overabundance of predominantly autotrophic nitrifiers, especially Nitrosopumilus, and oligotrophic marine Gammaproteobacteria in the Troll metagenomes compared to the Oslofjord. Increased potential for degradation of hydrocarbons, especially aromatic hydrocarbons, was detected in two of the Troll samples: one pockmark sample and one from the plain seabed. Although presence of methanotrophic organisms was indicated in all samples, no overabundance in pockmark samples compared to the Oslofjord samples supports no, or only low level, methane seepage in the Troll pockmarks at the present time. Conclusions Given the relatively low content of total organic carbon and great depths of hydrocarbon containing sediments in the Troll area, it is possible that at least part of the carbon source available for the predominantly autotrophic nitrifiers thriving in this area originates from sequential prokaryotic degradation and oxidation of hydrocarbons to CO2. By turning CO2 back into organic carbon this subcommunity could play an important environmental role in these dark oligotrophic sediments. The oxidation of ammonia to nitrite and nitrate in this process could further increase the supply of terminal electron acceptors for hydrocarbon degradation.

• Bråte, Jon; Krabberød, Anders Kristian; Dolven, Jane Karine Lønne; Ose, Randi Frida; Kristensen, Tom & Bjørklund, Kjell Rasmus [Show all 7 contributors for this article] (2012). Radiolaria Associated with Large Diversity of Marine Alveolates. Protist. ISSN 1434-4610. 163(5), p. 767–777. doi: 10.1016/j.protis.2012.04.004. Full text in Research Archive Show summary

  We have isolated cells of unculturable radiolarians from marine coastal waters. Individual cells were subjected to single cell whole genome amplification (SCWGA) and gene-targeted PCR. Using this approach we recover a surprisingly large diversity of sequences related to the enigmatic marine alveolate groups 1 and 2 (MALV I and MALV II) that most likely represent intracellular symbionts or parasites of the radiolarian cells. 18S rDNA phylogeny of the MALV sequences reveals 4 distinct clades of radiolarian associates here named Radiolarian Associated Sequences (RAS) 1-4. One clade of both phaeodarian and radiolarian associates and one clade of only phaeodarian associates are also identified. The MALV sequences cluster according to host type, i.e. sequences from associates identified in radiolarians, fish, copepods, ciliates or dinoflagellates are not intermixed but separated into distinct clades. This implies several independent colonizations of host lineages and links a large diversity of MALV to radiolarian-associated species. This demonstrates that radiolarians may be an important reservoir for MALV, making them a key group for understanding the impact of intracellular symbionts on the marine ecosystem. This study shows that applying SCWGA on unculturable cells is a promising approach to study the vast diversity and interactions of intracellular eukaryote organisms.

• Krabberød, Anders Kristian; Bråte, Jon; Dolven, Jane Karine Lønne; Ose, Randi Frida; Klaveness, Dag & Kristensen, Tom [Show all 8 contributors for this article] (2011). Radiolaria Divided into Polycystina and Spasmaria in Combined 18S and 28S rDNA Phylogeny. PLOS ONE. 6(8). doi: 10.1371/journal.pone.0023526. Full text in Research Archive Show summary

  Radiolarians are marine planktonic protists that belong to the eukaryote supergroup Rhizaria together with Foraminifera and Cercozoa. Radiolaria has traditionally been divided into four main groups based on morphological characters; i.e. Polycystina, Acantharia, Nassellaria and Phaeodaria. But recent 18S rDNA phylogenies have shown that Phaeodaria belongs within Cerocozoa, and that the previously heliozoan group Taxopodida should be included in Radiolaria. 18S rDNA phylogenies have not yet resolved the sister relationship between the main Radiolaria groups, but nevertheless suggests that Spumellaria, and thereby also Polycystina, are polyphyletic. Very few sequences other than 18S rDNA have so far been generated from radiolarian cells, mostly due to the fact that Radiolaria has been impossible to cultivate and single cell PCR has been hampered by low success rate. Here we have therefore investigated the mutual evolutionary relationship of the main radiolarian groups by using the novel approach of combining single cell whole genome amplification with targeted PCR amplification of the 18S and 28S rDNA genes. Combined 18S and 28S phylogeny of sequences obtained from single cells shows that Radiolaria is divided into two main lineages: Polycystina (Spumellaria+Nassellaria) and Spasmaria (Acantharia+Taxopodida). Further we show with high support that Foraminifera groups within Radiolaria supporting the Retaria hypothesis.

• Håvelsrud, Othilde Else; Haverkamp, Thomas Hendricus Augustus; Kristensen, Tom; Jakobsen, Kjetill Sigurd & Rike, Anne Gunn Larsen (2011). A metagenomic study of methanotrophic microorganisms in Coal Oil Point seep sediments. BMC Microbiology. 11. doi: 10.1186/1471-2180-11-221. Full text in Research Archive
• Rounge, Trine Ballestad; Rohrlack, Thomas; Decenciere, Fernandiere Beatriz; Edvardsen, Bente; Kristensen, Tom & Jakobsen, Kjetill Sigurd (2010). SUBPOPULATION DIFFERENTIATION ASSOCIATED WITH NONRIBOSOMAL PEPTIDE SYNTHETASE GENE CLUSTER DYNAMICS IN THE CYANOBACTERIUM PLANKTOTHRIX SPP.1. Journal of Phycology. ISSN 0022-3646. 46(4), p. 645–652. doi: 10.1111/j.1529-8817.2010.00856.x. Full text in Research Archive
• Rounge, Trine Ballestad; Rohrlack, Thomas; Nederbragt, Alexander Johan; Kristensen, Tom & Jakobsen, Kjetill Sigurd (2009). A genome-wide analysis of nonribosomal peptide synthetase gene clusters and their peptides in a Planktothrix rubescens strain. BMC Genomics. 10. doi: 10.1186/1471-2164-10-396. Full text in Research Archive Show summary

  Background Cyanobacteria often produce several different oligopeptides, with unknown biological functions, by nonribosomal peptide synthetases (NRPS). Although some cyanobacterial NRPS gene cluster types are well described, the entire NRPS genomic content within a single cyanobacterial strain has never been investigated. Here we have combined a genome-wide analysis using massive parallel pyrosequencing ("454") and mass spectrometry screening of oligopeptides produced in the strain Planktothrix rubescens NIVA CYA 98 in order to identify all putative gene clusters for oligopeptides. Results Thirteen types of oligopeptides were uncovered by mass spectrometry (MS) analyses. Microcystin, cyanopeptolin and aeruginosin synthetases, highly similar to already characterized NRPS, were present in the genome. Two novel NRPS gene clusters were associated with production of anabaenopeptins and microginins, respectively. Sequence-depth of the genome and real-time PCR data revealed three copies of the microginin gene cluster. Since NRPS gene cluster candidates for microviridin and oscillatorin synthesis could not be found, putative (gene encoded) precursor peptide sequences to microviridin and oscillatorin were found in the genes mdnA and oscA, respectively. The genes flanking the microviridin and oscillatorin precursor genes encode putative modifying enzymes of the precursor oligopeptides. We therefore propose ribosomal pathways involving modifications and cyclisation for microviridin and oscillatorin. The microviridin, anabaenopeptin and cyanopeptolin gene clusters are situated in close proximity to each other, constituting an oligopeptide island. Conclusion Altogether seven nonribosomal peptide synthetase (NRPS) gene clusters and two gene clusters putatively encoding ribosomal oligopeptide biosynthetic pathways were revealed. Our results demonstrate that whole genome shotgun sequencing combined with MS-directed determination of oligopeptides successfully can identify NRPS gene clusters and the corresponding oligopeptides. The analyses suggest independent evolution of all NRPS gene clusters as functional units. Our data indicate that the Planktothrix genome displays evolution of dual pathways (NRPS and ribosomal) for production of oligopeptides in order to maximize the diversity of oligopeptides with similar but functional discrete bioactivities.

• Ellefsen, Stian; Stensløkken, Kåre-Olav; Fagernes, Cathrine Elisabeth; Kristensen, Tom & Nilsson, Gøran Erik (2009). Expression of genes involved in GABAergic neurotransmission in anoxic crucian carp brain (Carassius carassius). Physiological Genomics. ISSN 1094-8341. 36(2), p. 61–68. doi: 10.1152/physiolgenomics.90301.2008. Full text in Research Archive
• Fewer, DP; Tooming-Klunderud, Ave; Jokela, J; Wahsten, M; Rouhiainen, L & Kristensen, Tom [Show all 9 contributors for this article] (2008). Natural occurrence of microcystin synthetase deletion mutants capable of producing microcystins in strains of the genus Anabaena (Cyanobacteria). Microbiology (Reading). ISSN 1350-0872. 154, p. 1007–1014. doi: 10.1099/mic.0.2007/016097-0. Full text in Research Archive
• Tooming-Klunderud, Ave; Fewer, DP; Rohrlack, Thomas; Jokela, J; Rouhiainen, L & Sivonen, K [Show all 8 contributors for this article] (2008). Evidence for positive selection acting on microcystin synthetase adenylation domains in three cyanobacterial genera. BMC Evolutionary Biology. 8. doi: 10.1186/1471-2148-8-256. Full text in Research Archive
• Ellefsen, Stian; Stenslokken, KO; Sandvik, Guro Katrine; Kristensen, Tom & Nilsson, Gøran Erik (2008). Improved normalization of real-time reverse transcriptase polymerase chain reaction data using an external RNA control. Analytical Biochemistry. ISSN 0003-2697. 376. doi: 10.1016/j.ab.2008.01.028. Full text in Research Archive
• Rounge, Trine Ballestad; Rohrlack, Thomas; Kristensen, Tom & Jakobsen, Kjetill Sigurd (2008). Recombination and selectional forces in cyanopeptolin NRPS operons from highly similar, but geographically remote Planktothrix strains. BMC Microbiology. 8. doi: 10.1186/1471-2180-8-141. Full text in Research Archive Show summary

  Background Cyanopeptolins are nonribosomally produced heptapetides showing a highly variable composition. The cyanopeptolin synthetase operon has previously been investigated in three strains from the genera Microcystis, Planktothrix and Anabaena. Cyanopeptolins are displaying protease inhibitor activity, but the biological function(s) is (are) unknown. Cyanopeptolin gene cluster variability and biological functions of the peptide variants are likely to be interconnected. Results We have investigated two cyanopeptolin gene clusters from highly similar, but geographically remote strains of the same genus. Sequencing of a nonribosomal peptide synthetase (NRPS) cyanopeptolin gene cluster from the Japanese strain Planktothrix NIES 205 (205-oci), showed the 30 kb gene cluster to be highly similar to the oci gene cluster previously described in Planktothrix NIVA CYA 116, isolated in Norway. Both operons contained seven NRPS modules, a sulfotransferase (S) and a glyceric acid loading (GA)-domain. Sequence analyses showed a high degree of conservation, except for the presence of an epimerase domain in NIES 205 and the regions around the epimerase, showing high substitution rates and Ka/Ks values above 1. The two strains produce almost identical cyanopeptolins, cyanopeptolin-1138 and oscillapeptin E respectively, but with slight differences regarding the production of minor cyanopeptolin variants. These variants may be the result of relaxed adenylation (A)-domain specificity in the nonribosomal enzyme complex. Other genetic markers (16S rRNA, ntcA and the phycocyanin cpcBA spacer) were identical, supporting that these geographically separated Planktothrix strains are closely related. Conclusion A horizontal gene transfer event resulting in exchange of a whole module-encoding region was observed. Nucleotide statistics indicate that both purifying selection and positive selection forces are operating on the gene cluster. The positive selection forces are acting within and around the epimerase insertion while purifying selection conserves the remaining (major) part of the gene cluster. The presence of an epimerase in the gene cluster is in line with the D-configuration of Htyr, determined experimentally in oscillapeptin E in a previous study.

• Tooming-Klunderud, Ave; Mikalsen, Bjørg; Kristensen, Tom & Jakobsen, Kjetill Sigurd (2008). The mosaic structure of the mcyABC operon in Microcystis. Microbiology (Reading). ISSN 1350-0872. 154, p. 1886–1899. doi: 10.1099/mic.0.2007/015875-0. Full text in Research Archive
• Ellefsen, Stian; Sandvik, Guro Katrine; Larsen, Helene Kile; Stensløkken, Kåre-Olav; Hov, Dag Are Steenhoff & Kristensen, Tom [Show all 7 contributors for this article] (2008). Expression of genes involved in excitatory neurotransmission in anoxic crucian carp (Carassius carassius) brain. Physiological Genomics. ISSN 1094-8341. 35, p. 5–17. Full text in Research Archive
• Rounge, Trine Ballestad; Rohrlack, Thomas; Tooming-Klunderud, Ave; Kristensen, Tom & Jakobsen, Kjetill Sigurd (2007). Comparison of cyanopeptolin genes in Planktothrix, Microcystis, and Anabaena strains: Evidence for independent evolution within each genus. Applied and Environmental Microbiology. ISSN 0099-2240. 73, p. 7322–7330. doi: 10.1128/AEM.01475-07. Full text in Research Archive
• Tooming-Klunderud, Ave; Rohrlack, Thomas; Shalchian-Tabrizi, Kamran; Kristensen, Tom & Jakobsen, Kjetill Sigurd (2007). Structural analysis of a non-ribosomal halogenated cyclic peptide and its putative operon from Microcystis: implications for evolution of cyanopeptolins. Microbiology (Reading). ISSN 1350-0872. 153(5), p. 1382–1393. doi: 10.1099/mic.0.2006/001123-0. Full text in Research Archive
• Soucek, Pavel; Skjelbred, Camilla Furu; Svendsen, Marit; Kristensen, Tom Arne; Kure, Elin H. & Kristensen, Vessela N. (2004). Single-track sequencing for genotyping of multiple SNPs in the N-acetyltransferase 1 (NAT1) gene. BMC Biotechnology. 4. doi: 10.1186/1472-6750-4-28. Full text in Research Archive Show summary

  Conclusions: The method could be of great help to scientists in the field of molecular epidemiology of screening of large populations for known informative biomarkers of susceptibility, such as NAT1. Background Fast, cheap and reliable methods are neededto identify large populations, which may be at risk in relation to environmental exposure. Polymorphisms in NAT1 (N-acetyl transferase) may be suitable markers to identify individuals at risk. Results A strategy allowing to address simultaneously 24 various genetic variants in the NAT1 gene usingthe single sequencing reaction method on the same PCR product is described. A modified automated DNA sequencing using only one of the sequence terminators was used to genotype PCR products in single-track sequencing reactions of NAT1 and was shown to be universal for both DNA sequencing using labeled primers and labeled nucleotides. By this method we detected known SNPs at site T640G, which confers the NAT1*11 allele with frequency of 0.036, further T1088A and C1095A with frequency of 0.172 and 0.188, respectively and a deletion of TAATAATAA in the poly A signal area with a frequency 0.031. All observed frequencies were in Hardy Weinberg equilibrium and comparable to those in Caucasian population. The single-track signatures of the variant genotypes were verified on samples previously genotyped by RLFP. Conclusions The method could beof great help to scientists in the field of molecular epidemiology of screening of large populations for known informative biomarkers of susceptibility, such as NAT1.

• Soucek, P; Gut, Ivan; Trneny, M; Skovlund, Eva; Alnæs, Grethe I. & Kristensen, Tom Arne [Show all 8 contributors for this article] (2003). Multiplex single-tube screening for mutations in the Nijmegen Breakage Syndrome (NBS1) gene in Hodgkin's and non-Hodgkin's lymphoma patients of Slavic origin. European Journal of Human Genetics. ISSN 1018-4813. 11(5), p. 416–419. Full text in Research Archive
• Huynh, Ngoc Trang Thi; Vad, Randi; Kristensen, Tom & Øyen, Tordis Beate (2001). The Genes of Two G-Proteins Involved in Protein Transport in Pichia pastoris. Biochemical and Biophysical Research Communications - BBRC. ISSN 0006-291X. 280(2), p. 454–459. Full text in Research Archive
• Kristensen, Vessela Nedelcheva; Harada, Nobuhiro; Kristensen, Tom Arne & Børresen-Dale, Anne-Lise (2001). Genetic polymorphism and variation in steroid hormone metabolism.: connection with risk of developing breast neoplasms, Vopr. Onkol. p. 156–159. Full text in Research Archive
• Kristensen, Vessela Nedelcheva; Kelefiotis, Dimitris; Kristensen, Tom Arne & Børresen-Dale, Anne-Lise (2001). High-throughput methods for detection of genetic variation. BioTechniques. ISSN 0736-6205. 30, p. 318–332. Full text in Research Archive Show summary

  High-Throughput Methods for Detection of Genetic Variation Understanding human genetic variation is currently believed to reveal the cause of individual susceptibility to disease and the large variation observed in response to treatment. In this review, we will focus on different approaches to identify and visualize genetic alterations. The various approaches for allele discrimination are formally systematically divided into (i) enzymatic approaches, in which the properties of different enzymes to discriminate between nucleotides are used (restriction enzymes type II, Cleavase and Resolvase, DNA polymerase, and ligase); (ii) electrophoretic methods, in which the allele discrimination is based on the difference in mobility in polymeric gels or capillaries (single- and double-stranded conformation assays, heteroduplex analysis, and DNA sequencing); (iii) solid-phase determination of allelic variants, including high-density oligonucleotide arrays for hybridization analysis, minisequencing primer extension analysis, and fiberoptic DNA sensor array; (iv) chromatographic methods such as denaturing high-performance liquid chromatography (DHPLC); (v) other physical methods of discrimination of allelic variants such as mass spectrometry (mass and charge) or fluorescence exchange-based techniques; and (vi) in silico methods such as high-throughput analysis of expressed sequence tag data. The most frequently used techniques and instrumental settings applied in different combinations are described, and other methods that are less broadly used but have interesting potentials are discussed.

• Tveit, Heidi & Kristensen, Tom Arne (2001). A fluorescence-based DNA polymerase assay. Analytical Biochemistry. ISSN 0003-2697. 189, p. 96–98. Full text in Research Archive Show summary

  The standard procedure for assaying DNA polymerase activity involves use of DNase treated DNA ("activated DNA") as a primer/template and incorporation of radioactive nucleotides into DNA (1). Measurement of acid-precipitable radioactivity relative to total radioactivity allows calculation of the amount of nucleotides incorporated and the number of enzyme units present (one unit of DNA polymerase activity is conventionally defined as the amount of enzyme that will incorporate 10 nmoles of nucleotides during a 30 minutes incubation). However, use of radioactivity is restricted and discouraged in many laboratories, and there is a general trend away from radioactivity-based techniques. For DNA polymerases, a commercial assay based on ELISA detection of digoxigenin-labelled nucleotides incorporated into newly made DNA is available (Roche Molecular Biochemicals, Cat No. 1669885). Also a fluorescence-based assay for DNA polymerase holoenzyme, based on the specific reaction of the dye PicoGreen® with double-stranded DNA, has been published (2). We have modified this procedure to make it suitable for less processive and complex DNA polymerase systems. The method described here allows quantitation of polymerase activity in preparations of family A and B polymerases at reaction temperatures between 37 and 72 °C, exemplified by the Klenow fragment of DNA polymerase I from E. coli, Taq DNA polymerase and Vent® polymerase.

• Huynh, Trang Thi Ngoc; Vad, Randi; Kristensen, Tom Arne & Øyen, Tordis Beate (2001). The genes of two G-proteins involved in protein transport in Pichia pastoris. Biochemical and Biophysical Research Communications - BBRC. ISSN 0006-291X. 180(2), p. 454–459. Full text in Research Archive Show summary

  Members of the Rab protein family play essential roles in vesicle fusion during protein secretion and represent highly conserved GTP binding proteins. The Saccharomyces cerevisiae Sec4p and Ypt1p, promoting vesicle fusion at the plasma membrane and in ER-Golgi transport, respectively, are among the best characterised yeast members. We have here cloned the Pichia pastoris SEC4 homologue using a S. cerevisiae SEC4 probe. In addition we isolated a crosshybridising clone encoding another Rab-/Ypt-like protein. The deduced full-length Pp Sec4p comprises 204 amino acid residues with an over all identity of 64% to the Sec4p from S. cerevisiae and 72% to the Candida albicans Sec4p. The YPT-like gene encodes a 216 amino acid residue protein showing highest similarity to the S. cerevisiae Ypt10p and Ypt53p. Both Pp Sec4p and the Ypt-like protein carry a -Cys-Cys C-terminus, indicating that these proteins are targets for geranyl-geranylation by a type II prenyltransferase.

• Warsame, Abdirashid; Vad, Randi; Kristensen, Tom Arne & Øyen, Tordis Beate (2001). Characterisation of a gene encoding a Pichia pastoris protein disulphide isomerase (PpPDI). Biochemical and Biophysical Research Communications - BBRC. ISSN 0006-291X. 281, p. 1176–1182. Full text in Research Archive Show summary

  Protein disulphide isomerases are multifunctional proteins belonging to the thioredoxin superfamily of protein-thiol oxidoreductases that have two double-cysteine redox-active sites and take part in protein folding in the endoplasmic reticulum (ER). We have used a Saccharomyces cerevisiae PDI hybridisation probe and report here the cloning of a Pichia pastoris genomic DNA fragment (2919 bp) that encodes the full length of a putative protein disulphide isomerase (PpPDI). The deduced protein sequence consists of 517 amino acid residues with a calculated molecular weight of 57788 and pI 4,4. It contains the two characteristic redox-active domains of the PDI-type -CGHC-, separated by 338 residues, and there are two potential N-glycosylation sites. The N-terminal end forms a putative signal sequence, and a possible calcium binding domain is represented by an acidic C-terminal region. Together with an ER retrieval sequence at the C-terminus, -HDEL, these features indicate that the gene encodes a redox-active ER-resident protein disulphide isomerase. The cloned fragment also encodes the C-terminal part, 142 amino acid residues, of a putative mitochondrial ribosomal protein and the full length of a 127-residue conserved hypothetical protein.

• Kristensen, V. N.; Kristensen, Vessela Nedelcheva; Kristensen, T.; Børresen-Dale, Anne-Lise & Kristensen, Tom Arne (2001). Hypervariable area in the 5´flanking region of GSTP1, previously reported as a minisatellite ATAAA repeat. Human Mutation. ISSN 1059-7794. 17, p. 238–239. Full text in Research Archive Show summary

  Known polymorphisms in the GSTP1 are point mutations in codon 104 and codon 113, possibly leading to changes in the kinetic properties of the enzyme and a repeat of ATAAA in the 5´ untranslated region (Smith et al. 1995), immediately upstream of an extensively methylated CpG island (Millar et al. 1999, Millar et al. 2000). Here we report that the repeat in the AT-rich area of the 5´ untranslated region is further degenerated by insertions of CAC, ATT, AAA and other motifs. The sequence alignments of the different allele sequences showed that in addition to the previously known repeat motif, there is a deletion of A and an insertion of ACACAA (also appearing in a sequence submitted to the GeneBank database, HUMGSTP1G Accession Nr.M24485), ATAA or ATTAA instead of ATAAA, as in allele E. Many of these alleles cannot be distinguished by size alone as allele A and C, B and L and D and H have the same length, and therefore the repeat has not been precisely characterised until now. In order to characterize the allele frequencies in larger control population we developed a fast heteroduplex analysis protocol. Simple electrophoretic run of PCR products in short polyacrylamide gels revealed the existence of 23 genotypes in Norwegian population based on different mobility of the PCR products of the different alleles as well as the formed heteroduplexes verified by DNA sequencing. The existence of distinctive degenerated alleles was also verified using three AT (Ataxia telangiectasia) families. Samples from father, mother and a child from each family revealed Mendelian inheritance of the variant alleles.

• Kristensen, Vessela Nedelcheva; Harada, Nobuhiro; Yoshimura, Noriko; Haraldsen, Ellen Christine; Lønning, Per Eystein & Erikstein, Bjørn [Show all 9 contributors for this article] (2000). Genetic variants of CYP19 (aromatase) and breast cancer risk. Oncogene. ISSN 0950-9232. 19(10), p. 1329–1333. Full text in Research Archive Show summary

  The effect of a SNP in exon 10 of CYP19 on tumor mRNA levels and splice variants were studied and correlated with clinical parameters and risk of breast cancer. In the vast majority of breast cancers, the estrogen levels modulate the tumor growth and depend on the activity of CYP19. Patients (n=481) and controls (n=236) were genotyped by T-tracks in a single sequencing reaction (SSR). The frequency of TT genotypes was significantly higher in patients versus controls (P=0.007) particularly among those with stage III and IV disease (P=0.004) and with tumors larger than 5 cm (P=0.001). A significant association between presence of the T allele and the level of aromatase mRNA in the tumors was observed (P=0.018), as well as with a switch from adipose promoter to ovary promoter (P=0.004). Previously, we reported a rare polymorphic allele of CYP19 (repeat (TTTA)12) to be significantly more frequent in breast cancer patients than in controls. Here we describe another polymorphism, a C ¿ T substitution in exon 10 of the CYP19 gene which is in strong linkage disequilibrium with the (TTTA)n polymorphism but with higher frequency of the variant allele. Our data suggest that the T-allele of the CYP19 gene is associated with a 'high activity' phenotype.

• Kristensen, Tom Arne; Kristensen, Vessela Nedelcheva & Børresen-Dale, Anne-Lise (2000). High-throughput screening for known mutations by automated analysis of single sequencing reactions. In Burczak, John D. & Mardis, Elaine (Ed.), Polymorphism Detection & Analysis. Eaton Publishing, Natick MA, USA. ISSN 9781881299479. p. 61–67. Full text in Research Archive Show summary

  The present work shows that single sequencing reactions analyzed on an automated DNA sequencer can be an efficient way of screening PCR products for known mutations. We have analyzed a mutation in exon 10 of the human aromatase gene and show that an unambiguous genotype could be elucidated in more than 90 % of the analyzed samples. Compared to analysis by full sequencing, 4 times more samples can be analyzed per gel, so that the sample capacity of the gel is approaching that of alternative gel-based methods for genotype analysis. Unlike many of these, the method offers direct identification of the variant sequence position and on-line analysis without the need of post-electrophoretic processing of the gel.

• Kristensen, Vessela Nedelcheva; Harada, Nobuhiro; Yoshimura, Noriko; Haraldsen, E.; Lønning, Per Eystein & Erikstein, Bjørn [Show all 9 contributors for this article] (2000). Genetic variants of CYP19 (arometase) and breast cancer risk. Oncogene. ISSN 0950-9232. 19(10), p. 1329–1333. Full text in Research Archive
• Kristensen, Tom Arne; Kristensen, Vessela Nedelcheva & Børresen-Dale, Anne-Lise (1998). High-thorughput screening for known mutations by automated analysis of single sequencing reaction. BioTechniques. ISSN 0736-6205. 24, p. 832–835. Full text in Research Archive
• Kristensen, Tom Arne; Kristensen, Vessela Nedelcheva & Børresen-Dale, Anne-Lise (1998). High-throughput screening for known mutations by automated analysis of single sequencing reactions. BioTechniques. ISSN 0736-6205. 24, p. 832–835. Full text in Research Archive
• Nasir, Achmad I.; Gundersen, Lise-Lotte; Rise, Frode; Antonsen, Øyvind; Kristensen, Tom Arne & Langhelle, B. [Show all 10 contributors for this article] (1998). Inhibition of Lipid Peroxidation mediated by Indolizines. Bioorganic & Medicinal Chemistry Letters. ISSN 0960-894X. p. 1828–1832. Full text in Research Archive Show summary

  http://folk.uio.no/froderi/Indolizin.pdf

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• Bustad, Helene J.; Flydal, Marte Innselset; Knævelsrud, Helene; Langaker, Ann Helen; Boye, Erik & Kristensen, Tom (2022). Slik utvikler vi norske fagtermer i celle-og molekylærbiologi. Tidsskrift for Den norske legeforening (Tidsskriftet). ISSN 0029-2001. 142(2). doi: 10.4045/tidsskr.21.0465. Full text in Research Archive
• Bustad, Helene J.; Flydal, Marte Innselset; Knævelsrud, Helene; Boye, Erik & Kristensen, Tom Arne (2021). Et kappløp for norsk fagspråk. Michael. ISSN 1893-9651. 18(26), p. 81–91. Full text in Research Archive
• Kristensen, Tom; Nissen-Meyer, Jon; Oppegård, Camilla; Ekblad, Bie; Kjos, Morten & Diep, Dzung Bao [Show all 7 contributors for this article] (2015). Whole genome sequencing as a tool to elucidate the mechanism of action of AMPs. Full text in Research Archive
• Kristensen, Tom; Kjos, Morten; Oppegård, Camilla; Diep, Dzung Bao; Nes, Ingolf & Nissen-Meyer, Jon (2014). Identification of bacteriocin resistance-inducing mutations by whole genome sequencing without a reference genome: The putative receptor of plantaricin JK. Full text in Research Archive
• Oppegård, Camilla; Kjos, Morten; Diep, Dzung Bao; Nes, Ingolf; Veening, Jan-Willem & Nissen-Meyer, Jon [Show all 7 contributors for this article] (2014). Genome sequencing of lactococcin G-resistant strains identified UppP, an enzyme involved in cell wall synthesis, as a putative bacteriocin receptor. Full text in Research Archive
• Kristensen, Tom (2013). Bioteknologi - til glede og fortvilelse. Full text in Research Archive
• Kristensen, Tom; Nissen-Meyer, Jon; Diep, Dzung Bao; Oppegård, Camilla; Nes, Ingolf & Kjos, Morten (2013). Genomic sequencing as a tool to identify bacteriocin receptors. Full text in Research Archive
• Rike, Anne Gunn Larsen; Håvelsrud, Othilde Else; Haverkamp, Thomas Hendricus Augustus; Kristensen, Tom & Jakobsen, Kjetill Sigurd (2013). Metagenomics in methane seep detection and studies of the microbial methane sediment filter. Full text in Research Archive
• Nissen-Meyer, Jon; Kristensen, Tom; Diep, Dzung Bao & Nes, Ingolf (2012). Bakteriosiner: En gruppe antimikrobielle peptider med et stort potensial til å bekjempe patogene bakterier. NBS-nytt. ISSN 0801-3535. 3. Full text in Research Archive
• Bråte, Jon; Krabberød, Anders Kristian; Dolven, Jane Karine Lønne; Ose, Randi Frida; Kristensen, Tom & Bjørklund, Kjell Rasmus [Show all 7 contributors for this article] (2010). Diversity of unculturable Radiolaria and their symbionts revealed by 18S rDNA phylogeny. Full text in Research Archive
• Kristensen, Tom (2009). «Scavenger» – fjerner det som er uønsket. Tidsskrift for Den norske legeforening (Tidsskriftet). ISSN 0029-2001. 129(10), p. 1016–1016. doi: 10.4045/tidsskr.09.0362. Full text in Research Archive
• Kristensen, Tom (2005). Nobelprisen i kjemi. In Reisegg, Øyvind (Eds.), Aschehoug og Gyldendals Store Norske Årbok. Kunnskapsforlaget. ISSN 9788257316037. p. 444–446. Full text in Research Archive
• Antonsen, Øyvind Gunnar; Kristensen, Tom Arne; Langhelle, B.; Fosnes, K.; Larsen, V. & Gundersen, Lise-Lotte [Show all 10 contributors for this article] (2001). Synthesis of Indolizines and Pyrrolo[1,2-b]pyridazine with Antioxidant Properties. Full text in Research Archive
• Kristensen, Tom Arne; Kalleberg, Ingvild Berlin & Plagemann, Thomas Peter (2001). Implementing Configurable Signalling in the MULTE-ORB. Full text in Research Archive
• Kristensen, Tom Arne (2000). Kappløpet om genene. [Radio]. Oslo : NRK P2 radio. Full text in Research Archive Show summary

  Intervju om kappløpet mellom private og offentlige institusjoner om sekvensering av det humane genom

• Øyen, Tordis Beate; Jorde, A. T. & Kristensen, Tom Arne (2000). The iron-containing catalytic subunit of Pichia pastoris ribonucleotide reductase, RNR2. Full text in Research Archive
• Kristensen, Tom Arne (1999). DNA polymerases in PCR and DNA sequencing. Full text in Research Archive
• Kristensen, Tom Arne (1999). DNA polymerases in PCR and DNA sequencing. Full text in Research Archive
• Kristensen, Vessela Nedelcheva; Harada, Nobuhiro; Haraldsen, Ellen Christine; Yoshimura, Noriko; Lønning, Per Eystein & Erikstein, Bjørn [Show all 9 contributors for this article] (1999). GENETIC POLYMORPHISMS OF CYP19 (AROMATASE), BREAST CANCER RISK AND CLINICAL AND HISTOPATHOLOGICAL PARAMETERS. Full text in Research Archive
• Kristensen, Tom Arne (1999). Biokjemi - hva er vitsen? Full text in Research Archive
• Kristensen, Vessela Nedelcheva; Harada, Nobuhiro; Haraldsen, Ellen Christine; Yoshimura, Noriko; Lønning, Per Eystein & Kristensen, Tom Arne [Show all 7 contributors for this article] (1999). GENETIC VARIANTS OF CYP19 (AROMATASE), mRNA LEVELS AND PUTATIVE STRUCTURE OF THE TRANSCRIPT. Full text in Research Archive
• Kristensen, Vessela Nedelcheva; Harada, Nobuhiro; Haraldsen, Ellen Christine; Yoshimura, Noriko; Lønning, Per Eystein & Kristensen, Tom Arne [Show all 7 contributors for this article] (1999). GENETIC VARIANTS OF CYP19 (AROMATASE), mRNA LEVELS AND PUTATIVE STRUCTURE. Full text in Research Archive
• Kristensen, Vessela Nedelcheva; Harada, Nobuhiro; Haraldsen, Ellen Christine; Yoshimura, Noriko; Lønning, Per Eystein & Erikstein, Bjørn [Show all 9 contributors for this article] (1999). GENETIC POLYMORPHISMS OF CYP19 (AROMATASE), BREAST CANCER RISK AND CLINICAL AND HISTOPATHOLOGICAL PARAMETERS. Full text in Research Archive
• Tvermyr, Marianne; Kristiansen, Bjørn Evert & Kristensen, Tom Arne (1999). PROOFREADING ACTIVITY OF FAMILY A DNA POLYMERASES: THERE FROM THE BEGINNING. Full text in Research Archive Show summary

  Eubacterial family A DNA polymerases are proteins with a single amino acid chain arranged in three domains. In E. coli DNA polymerase I, the most extensively characterized enzyme in the family, the N-terminal domain is associated with a 5'-3' exonuclease activity whereas the central domain is responsible for the proofreading 3'-5' exonuclease activity and the C-terminal domain for the nucleotide polymerizing activity. The N- and C-terminal domains and the associated enzymatic activities are generally well conserved in the family, whereas the central domain shows less sequence conservation. Comparing Taq DNA polymerase with the E. coli enzyme, for example, shows 31 % identical residues in the N-terminal domain and 48 % in the C-terminal domain, but only 14 % in the central domain. The corresponding proofreading activity also lacks in several family members, such as Taq DNA polymerase, B. stearotherophilus DNA polymerase I and S. pneumoniae DNA polymerase I. This has lead to the proposal that the ancestral polA gene only contained 5'-3' exonuclease activity in addition to its polymerase activity, and that the proofreading 3'-5' exonuclease activity more recently has been recruited into the gene in some eubacteria like E. coli. We have cloned and sequenced the polA gene of Chloroflexus aurantiacus, a green nonsulfur eubacterium which branched off early during eubacterial evolution. Comparing with the E. coli sequence we find that the central domain is almost as well conserved as the N-terminal domain (30 % identical residues compared to 33 %). In addition all amino acid residues and sequence motifs known to be important for the exonuclease activity are conserved. This may indicate that the ancestral polA gene coded for a protein with all three enzymatic activities, and that the proofreading activity has been lost several times independently during evolution.

• Kristensen, Tom Arne (1998). Hva er bioinformatikk? [Radio]. Forskning nr.7. : NRK. Full text in Research Archive
• Rønneberg, J. A.; Kristensen, Tom Arne; Larsen, Frank & Bosnes, M. (1997). Optimalization of the Tth DNA polymerase reverse transcriptase activity for the use with Dynabeads (R). Full text in Research Archive
• Kristiansen, Bjørn Evert & Kristensen, Tom Arne (1997). Expression of Chloroflexus aurantiacus DNA polymerase I in Eschericia coli. There from the beginning? Full text in Research Archive
• Kristensen, Tom Arne (1997). Verdt å vite. Full text in Research Archive
• Kristensen, Tom Arne (1996). intervju. [Radio]. Verdt og vite, NRK. Full text in Research Archive

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