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Persson, Bengt
Publications (10 of 60) Show all publications
Ostberg, L. J., Stromberg, P., Hedberg, J. J., Persson, B. & Hoog, J.-O. (2013). Analysis of mammalian alcohol dehydrogenase 5 (ADH5): Characterisation of rat ADH5 with comparisons to the corresponding human variant. Chemico-Biological Interactions, 202(1-3), 97-103
Open this publication in new window or tab >>Analysis of mammalian alcohol dehydrogenase 5 (ADH5): Characterisation of rat ADH5 with comparisons to the corresponding human variant
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2013 (English)In: Chemico-Biological Interactions, ISSN 0009-2797, E-ISSN 1872-7786, Vol. 202, no 1-3, p. 97-103Article in journal (Refereed) Published
Abstract [en]

Alcohol dehydrogenase 5 (ADH5) is a member of the mammalian alcohol dehydrogenase family of yet undefined functions. ADH5 was first identified at the DNA level in human and deer mouse. A rat alcohol dehydrogenase structure of similar type has been isolated at the cDNA level using human ADH5 as a screening probe, where the rat cDNA structure displayed several atypical properties. mRNA for rat ADH5 was found in multiple tissues, especially in the kidney. In vitro translation experiments indicated that rat ADH5 is expressed as efficiently as ADH1 and furthermore, rat ADH5 was readily expressed in COS cells fused to Green Fluorescent Protein. However, no soluble ADH5 protein could be heterologously expressed in Escherichia coil cells with expression systems successfully used for other mammalian ADHs, including fused to glutathione-S-transferase. Molecular modelling of the enzyme indicated that the protein does not fold in a productive way, which can be the explanation why no stable and active ADH5 has been isolated. These results indicate that ADH5, while readily expressed at the mRNA level, does not behave similarly to other mammalian ADHs investigated. The results, in vitro and in silico, suggest an unstable ADH5 structure, which can explain for why no active and stable protein can be isolated. Further possibilities are conceivable: the ADH5 protein may have to interact with a stabiliser, or the gene is actually a pseudogene.

Place, publisher, year, edition, pages
Elsevier, 2013
Keyword
Alcohol dehydrogenase, ADH classes, Enzyme family, Molecular modelling, Protein expression
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-93267 (URN)10.1016/j.cbi.2012.11.002 (DOI)000317539500013 ()
Note

Funding Agencies|Karolinska Institutet||Linkoping University||SeRC (Swedish eScience Research Centre)||

Available from: 2013-05-28 Created: 2013-05-28 Last updated: 2017-12-06
Persson, B. & Kallberg, Y. (2013). Classification and nomenclature of the superfamily of short-chain dehydrogenases/reductases (SDRs). Chemico-Biological Interactions, 202(1-3), 111-115
Open this publication in new window or tab >>Classification and nomenclature of the superfamily of short-chain dehydrogenases/reductases (SDRs)
2013 (English)In: Chemico-Biological Interactions, ISSN 0009-2797, E-ISSN 1872-7786, Vol. 202, no 1-3, p. 111-115Article in journal (Refereed) Published
Abstract [en]

The short-chain dehydrogenases/reductases (SDRs) constitute one of the largest protein superfamilies known today. The members are distantly related with typically 20-30% residue identity in pair-wise comparisons. Still, all hitherto structurally known SDRs present a common three-dimensional structure consisting of a Rossmann fold with a parallel beta sheet flanked by three helices on each side. Using hidden Markov models (HMMs), we have developed a semi-automated subclassification system for this huge family. Currently, 75% of all SDR forms have been assigned to one of the 464 families totalling 122,940 proteins. There are 47 human SDR families, corresponding to 75 genes. Most human SDR families (35 families) have only one gene, while 12 have between 2 and 8 genes. For more than half of the human SDR families, the three-dimensional fold is known. The number of SDR members increases considerably every year, but the number of SDR families now starts to converge. The classification method has paved the ground for a sustainable and expandable nomenclature system. Information on the SDR superfamily is continuously updated at http://sdr-enzymes.org/.

Place, publisher, year, edition, pages
ELSEVIER IRELAND LTD, ELSEVIER HOUSE, BROOKVALE PLAZA, EAST PARK SHANNON, CO, CLARE, 00000, IRELAND, 2013
Keyword
Short-chain dehydrogenases/reductases, Hidden Markov models, Functional assignment, Nomenclature, Classification, Bioinformatics
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-93268 (URN)10.1016/j.cbi.2012.11.009 (DOI)000317539500015 ()
Available from: 2013-05-28 Created: 2013-05-28 Last updated: 2017-12-06
Jornvall, H., Hedlund, J., Bergman, T., Kallberg, Y., Cederlund, E. & Persson, B. (2013). Origin and evolution of medium chain alcohol dehydrogenases. Chemico-Biological Interactions, 202(1-3), 91-96
Open this publication in new window or tab >>Origin and evolution of medium chain alcohol dehydrogenases
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2013 (English)In: Chemico-Biological Interactions, ISSN 0009-2797, E-ISSN 1872-7786, Vol. 202, no 1-3, p. 91-96Article in journal (Refereed) Published
Abstract [en]

Different lines of alcohol dehydrogenases (ADHs) have separate superfamily origins, already recognized but now extended and re-evaluated by re-screening of the latest databank update. The short-chain form (SDR) is still the superfamily with most abundant occurrence, most multiple divergence, most prokaryotic emphasis, and most non-complicated architecture. This pattern is compatible with an early appearance at the time of the emergence of prokaryotic cellular life. The medium-chain form (MDR) is also old but second in terms of all the parameters above, and therefore compatible with a second emergence. However, this step appears seemingly earlier than previously considered, and may indicate sub-stages of early emergences at the increased resolution available from the now greater number of data entries. The Zn-MDR origin constitutes a third stage, possibly compatible with the transition to oxidative conditions on earth. Within all these three lines, repeated enzymogeneses gave the present divergence. MDR-ADH origin(s), at a fourth stage, may also be further resolved in multiple or extended modes, but the classical liver MDR-ADH of the liver type can still be traced to a gene duplication similar to 550 MYA (million years ago), at the early vertebrate radiation, compatible with the post-eon-shift, "Cambrian explosion". Classes and isozymes correspond to subsequent and recent duplicatory events, respectively. They illustrate a peculiar pattern with functional and emerging evolutionary distinctions between parent and emerging lines, suggesting a parallelism between duplicatory and mutational events, now also visible at separate sub-stages. Combined, all forms show distinctive patterns at different levels and illustrate correlations with global events. They further show that simple molecular observations on patterns, multiplicities and occurrence give much information, suggesting common divergence rules not much disturbed by horizontal gene transfers after the initial origins.

Place, publisher, year, edition, pages
Elsevier, 2013
Keyword
Databank screening, Molecular evolution, Metalloenzyme acquirement, Restricted co-evolution, MDR, SDR
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-93266 (URN)10.1016/j.cbi.2012.11.008 (DOI)000317539500012 ()
Note

Funding Agencies|Swedish Research Council||Karolinska Institutet||Karolinska Institutet, Department of Medical Biochemistry and Biophysics||Linkoping University||

Available from: 2013-05-28 Created: 2013-05-28 Last updated: 2017-12-06
Bzhalava, D., Johansson, H., Ekstrom, J., Faust, H., Moller, B., Eklund, C., . . . Dillner, J. (2013). Unbiased Approach for Virus Detection in Skin Lesions. PLoS ONE, 8(6)
Open this publication in new window or tab >>Unbiased Approach for Virus Detection in Skin Lesions
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2013 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 6Article in journal (Refereed) Published
Abstract [en]

To assess presence of virus DNA in skin lesions, swab samples from 82 squamous cell carcinomas of the skin (SCCs), 60 actinic keratoses (AKs), paraffin-embedded biopsies from 28 SCCs and 72 kerathoacanthomas (KAs) and fresh-frozen biopsies from 92 KAs, 85 SCCs and 92 AKs were analyzed by high throughput sequencing (HTS) using 454 or Ion Torrent technology. We found total of 4,284 viral reads, out of which 4,168 were Human Papillomavirus (HPV)-related, belonging to 15 known (HPV8, HPV12, HPV20, HPV36, HPV38, HPV45, HPV57, HPV59, HPV104, HPV105, HPV107, HPV109, HPV124, HPV138, HPV147), four previously described putative (HPV 915 F 06 007 FD1, FA73, FA101, SE42) and two putatively new HPV types (SE46, SE47). SE42 was cloned, sequenced, designated as HPV155 and found to have 76% similarity to the most closely related known HPV type. In conclusion, an unbiased approach for viral DNA detection in skin tumors has found that, although some new putative HPVs were found, known HPV types constituted most of the viral DNA.

Place, publisher, year, edition, pages
Public Library of Science, 2013
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-96427 (URN)10.1371/journal.pone.0065953 (DOI)000321148400009 ()
Note

Funding Agencies|Swedish Cancer Society|110569|Swedish Research Council|3468|Swedish government strategic program on Biomarkers in Cancer Research (BioCARE)||

Available from: 2013-08-20 Created: 2013-08-19 Last updated: 2017-12-06
Lysholm, F., Wetterbom, A., Lindau, C., Darban, H., Bjerkner, A., Fahlander, K., . . . Andersson, B. (2012). Characterization of the Viral Microbiome in Patients with Severe Lower Respiratory Tract Infections, Using Metagenomic Sequencing. PLoS ONE, 7(2)
Open this publication in new window or tab >>Characterization of the Viral Microbiome in Patients with Severe Lower Respiratory Tract Infections, Using Metagenomic Sequencing
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2012 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 2Article in journal (Refereed) Published
Abstract [en]

The human respiratory tract is heavily exposed to microorganisms. Viral respiratory tract pathogens, like RSV, influenza and rhinoviruses cause major morbidity and mortality from respiratory tract disease. Furthermore, as viruses have limited means of transmission, viruses that cause pathogenicity in other tissues may be transmitted through the respiratory tract. It is therefore important to chart the human virome in this compartment. We have studied nasopharyngeal aspirate samples submitted to the Karolinska University Laboratory, Stockholm, Sweden from March 2004 to May 2005 for diagnosis of respiratory tract infections. We have used a metagenomic sequencing strategy to characterize viruses, as this provides the most unbiased view of the samples. Virus enrichment followed by 454 sequencing resulted in totally 703,790 reads and 110,931 of these were found to be of viral origin by using an automated classification pipeline. The snapshot of the respiratory tract virome of these 210 patients revealed 39 species and many more strains of viruses. Most of the viral sequences were classified into one of three major families; Paramyxoviridae, Picornaviridae or Orthomyxoviridae. The study also identified one novel type of Rhinovirus C, and identified a number of previously undescribed viral genetic fragments of unknown origin.

Place, publisher, year, edition, pages
Public Library of Science, 2012
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:liu:diva-77340 (URN)10.1371/journal.pone.0030875 (DOI)000302741300031 ()
Note

Funding Agencies|Swedish Research Council|2010-3754|

Available from: 2012-05-11 Created: 2012-05-11 Last updated: 2017-12-07
Melkersson, K. & Persson, B. (2012). Evidence for a negative association between schizophrenia and a polymorphism in the insulin receptor substrate-3 (IRS-3) gene. Neuro - endocrinology letters, 33(3), 321-330
Open this publication in new window or tab >>Evidence for a negative association between schizophrenia and a polymorphism in the insulin receptor substrate-3 (IRS-3) gene
2012 (English)In: Neuro - endocrinology letters, ISSN 0172-780X, Vol. 33, no 3, p. 321-330Article in journal (Refereed) Published
Abstract [en]

OBJECTIVES: Since there are clear indications that schizophrenia is a systemic disorder, we sought for a common molecular basis for schizophrenia abnormalities in brain and body. Our hypothesis was that an impaired insulin and insulin-like growth factor signalling in cells might underlie changes in both brain and body in schizophrenia. In this regard, the insulin receptor substrates 1-4, linking both the insulin and insulin-like growth factor-1 receptors with intracellular pathways, might be of interest to study genetically. In the present study, we chose to study the insulin receptor substrate-3 (IRS-3) gene as a candidate gene in schizophrenia. less thanbrgreater than less thanbrgreater thanMETHODS: The IRS-3 gene of 93 patients with the diagnosis of schizophrenia according to DSM-IV criteria and 57 healthy control subjects was screened for DNA sequence variations, followed by case-control analyses of total 10 detected polymorphisms. less thanbrgreater than less thanbrgreater thanRESULTS: The A/G genotype of the single nucleotide polymorphism (SNP) rs117078492 in the IRS-3 gene occurred in 5.3% of the control subjects compared with in 0% of the patients (p=0.05). Similarly, the haplotypes 5 and 3X, constructed from polymorphisms in the IRS-3 gene and including the A allele of this A/G SNP, occurred only in the control subjects and not in the patients (5.3% vs 0%, p=0.05). less thanbrgreater than less thanbrgreater thanCONCLUSION: Our findings suggest that individuals carrying the A allele of this A/G SNP in the IRS-3 gene as well as the estimated haplotypes 5 or 3X including this A allele, have a protection against schizophrenia development.

Place, publisher, year, edition, pages
Brain Research Promotion, 2012
Keyword
case-control study, DNA sequencing, height, IRS-3, IRS-3P, psychotic disorder, schizophrenia, single nucleotide polymorphism
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-79114 (URN)10.1016/S0924-9338(13)77131-1 (DOI)000305102500019 ()
Note

Funding Agencies|Swedish Research Council||Swedish Society of Medicine||

Available from: 2012-06-29 Created: 2012-06-29 Last updated: 2017-12-07
Kallberg, Y., Segerstolpe, Å., Lackman, F., Persson, B. & Wieslander, L. (2012). Evolutionary Conservation of the Ribosomal Biogenesis Factor Rbm19/Mrd1: Implications for Function. PLoS ONE, 7(9)
Open this publication in new window or tab >>Evolutionary Conservation of the Ribosomal Biogenesis Factor Rbm19/Mrd1: Implications for Function
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2012 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 9Article in journal (Refereed) Published
Abstract [en]

Ribosome biogenesis in eukaryotes requires coordinated folding and assembly of a pre-rRNA into sequential pre-rRNA-protein complexes in which chemical modifications and RNA cleavages occur. These processes require many small nucleolar RNAs (snoRNAs) and proteins. Rbm19/Mrd1 is one such protein that is built from multiple RNA-binding domains (RBDs). We find that Rbm19/Mrd1 with five RBDs is present in all branches of the eukaryotic phylogenetic tree, except in animals and Choanoflagellates, that instead have a version with six RBDs and Microsporidia which have a minimal Rbm19/Mrd1 protein with four RBDs. Rbm19/Mrd1 therefore evolved as a multi-RBD protein very early in eukaryotes. The linkers between the RBDs have conserved properties; they are disordered, except for linker 3, and position the RBDs at conserved relative distances from each other. All but one of the RBDs have conserved properties for RNA-binding and each RBD has a specific consensus sequence and a conserved position in the protein, suggesting a functionally important modular design. The patterns of evolutionary conservation provide information for experimental analyses of the function of Rbm19/Mrd1. In vivo mutational analysis confirmed that a highly conserved loop 5-β4-strand in RBD6 is essential for function.

National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:liu:diva-81955 (URN)10.1371/journal.pone.0043786 (DOI)000308738500022 ()
Note

funding agencies|Swedish Research Council||Carl Tryggers Stiftelse||Linkoping University||

Available from: 2012-09-26 Created: 2012-09-26 Last updated: 2017-12-07
Carlsson, J. & Persson, B. (2012). Investigating protein variants using structural calculation techniques. In: Andrew J. W. Orry and Ruben Abagyan (Ed.), Homology Modeling: Methods and Protocols (pp. 313-330). Springer, 857
Open this publication in new window or tab >>Investigating protein variants using structural calculation techniques
2012 (English)In: Homology Modeling: Methods and Protocols / [ed] Andrew J. W. Orry and Ruben Abagyan, Springer, 2012, Vol. 857, p. 313-330Chapter in book (Other academic)
Abstract [en]

Knowledge about protein tertiary structure can guide experiments, assist in the understanding of structure-function relationships, and aid the design of new therapeutics for disease. Homology modeling is an in silico method that predicts the tertiary structure of an amino acid sequence based on a homologous experimentally determined structure. In, Homology Modeling: Methods and Protocols experts in the field describe each homology modeling step from first principles, provide case studies for challenging modeling targets and describe methods for the prediction of how other molecules such as drugs can interact with the protein. Written in the highly successful Methods in Molecular Biology series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, Homology Modeling: Methods and Protocols guides scientists in the available homology modeling methods.

Place, publisher, year, edition, pages
Springer, 2012
Series
Methods in Molecular Biology, ISSN 1064-3745, E-ISSN 1940-6029 ; 857
Keyword
Sequence alignment (Bioinformatics), Life sciences, Biochemistry, Protein Science, Protein Structure
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:liu:diva-81961 (URN)10.1007/978-1-61779-588-6_14 (DOI)978-1-61779-587-9 (ISBN)978-1-61779-588-6 (ISBN)
Available from: 2012-09-26 Created: 2012-09-26 Last updated: 2017-04-10Bibliographically approved
Bzhalava, D., Ekström, J., Lysholm, F., Hultin, E., Faust, H., Persson, B., . . . Dillner, J. (2012). Phylogenetically diverse TT virus viremia among pregnant women. Virology, 432(2), 427-434
Open this publication in new window or tab >>Phylogenetically diverse TT virus viremia among pregnant women
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2012 (English)In: Virology, ISSN 0042-6822, E-ISSN 1096-0341, Vol. 432, no 2, p. 427-434Article in journal (Refereed) Published
Abstract [en]

Infections during pregnancy have been suggested to be involved in childhood leukemias. We used high-throughput sequencing to describe the viruses most readily detectable in serum samples of pregnantwomen. Serum DNA of 112 mothers to leukemic children was amplified using whole genome amplification. Sequencing identified one TTvirus (TTV) isolate belonging to a known type and two putatively new TTVs. For 22 mothers, we also performed TTV amplification by general primer PCR before sequencing. This detected 39 TTVs, two of which were identical to the TTVs found after whole genome amplification.

Altogether, we found 40 TTV isolates, 29 of which were putatively new types (similarities ranging from 89% to 69%). In conclusion, high throughput sequencing is useful to describe the known or unknown viruses that are present in serum samples of pregnantwomen.

Place, publisher, year, edition, pages
Elsevier, 2012
Keyword
Childhood leukemia; TTvirus; High throughput sequencing
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:liu:diva-81957 (URN)10.1016/j.virol.2012.06.022 (DOI)000308121600021 ()
Note

funding agencies|European Union Network of Excellence Cancer Control using Population-based Registries and Biobanks||Swedish Cancer Society||Swedish Research Council||Karolinska Institutet||

Available from: 2012-09-26 Created: 2012-09-26 Last updated: 2017-12-07Bibliographically approved
Moummou, H., Kallberg, Y., Brice Tonfack, L., Persson, B. & van der Rest, B. (2012). The Plant Short-Chain Dehydrogenase (SDR) superfamily: genome-wide inventory and diversification patterns. BMC Plant Biology, 12(219)
Open this publication in new window or tab >>The Plant Short-Chain Dehydrogenase (SDR) superfamily: genome-wide inventory and diversification patterns
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2012 (English)In: BMC Plant Biology, ISSN 1471-2229, E-ISSN 1471-2229, Vol. 12, no 219Article in journal (Refereed) Published
Abstract [en]

Background: Short-chain dehydrogenases/reductases (SDRs) form one of the largest and oldest NAD(P)(H) dependent oxidoreductase families. Despite a conserved Rossmann-fold structure, members of the SDR superfamily exhibit low sequence similarities, which constituted a bottleneck in terms of identification. Recent classification methods, relying on hidden-Markov models (HMMs), improved identification and enabled the construction of a nomenclature. However, functional annotations of plant SDRs remain scarce. less thanbrgreater than less thanbrgreater thanResults: Wide-scale analyses were performed on ten plant genomes. The combination of hidden Markov model (HMM) based analyses and similarity searches led to the construction of an exhaustive inventory of plant SDR. With 68 to 315 members found in each analysed genome, the inventory confirmed the over-representation of SDRs in plants compared to animals, fungi and prokaryotes. The plant SDRs were first classified into three major types - classical, extended and divergent - but a minority (10% of the predicted SDRs) could not be classified into these general types (unknown or atypical types). In a second step, we could categorize the vast majority of land plant SDRs into a set of 49 families. Out of these 49 families, 35 appeared early during evolution since they are commonly found through all the Green Lineage. Yet, some SDR families - tropinone reductase-like proteins (SDR65C), ABA2-like-NAD dehydrogenase (SDR110C), salutaridine/menthone-reductase-like proteins (SDR114C), dihydroflavonol 4-reductase-like proteins (SDR108E) and isoflavone-reductase-like (SDR460A) proteins - have undergone significant functional diversification within vascular plants since they diverged from Bryophytes. Interestingly, these diversified families are either involved in the secondary metabolism routes (terpenoids, alkaloids, phenolics) or participate in developmental processes (hormone biosynthesis or catabolism, flower development), in opposition to SDR families involved in primary metabolism which are poorly diversified. less thanbrgreater than less thanbrgreater thanConclusion: The application of HMMs to plant genomes enabled us to identify 49 families that encompass all Angiosperms (higher plants) SDRs, each family being sufficiently conserved to enable simpler analyses based only on overall sequence similarity. The multiplicity of SDRs in plant kingdom is mainly explained by the diversification of large families involved in different secondary metabolism pathways, suggesting that the chemical diversification that accompanied the emergence of vascular plants acted as a driving force for SDR evolution.

Place, publisher, year, edition, pages
BioMed Central, 2012
Keyword
Short-chain dehydrogenase/reductase (SDRs), SDR nomenclature initiative, Hidden markov model, Multigenic family, Plant
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:liu:diva-88672 (URN)10.1186/1471-2229-12-219 (DOI)000313689900001 ()
Note

Funding Agencies|EGIDE|MA-06-155|Libert Brice Tonfack from "Service de Cooperation et dAction Culturelle" of the French Embassy (Cameroon)||

Available from: 2013-02-14 Created: 2013-02-14 Last updated: 2017-12-06
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