| 1. |
- Breuer, Judith, et al.
(author)
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A proposal for a common nomenclature for viral clades that form the genus varicella-zoster virus.
- 2010
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In: The Journal of general virology. - : Microbiology Society. - 1465-2099 .- 0022-1317. ; 91:4, s. 821-828
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Journal article (peer-reviewed)abstract
- Varicella zoster virus (VZV), the cause of chickenpox and zoster, was the first human herpesvirus to be sequenced fully and the first for which vaccines have been licensed and widely used. Three groups have published genotyping schemes based on single nucleotide polymorphisms (SNP) and between them identified five distinct phylogenetic clades, with an additional two putative clades . Sequencing of over 23 whole VZV genomes from around the world further refined the phylogenic distinctions between SNP genotypes. Widespread surveillance in countries in which varicella vaccine is now in use and the difficulties posed by three unique genotyping approaches, prompted an international meeting at which a common nomenclature based on phylogenetic clades , was agreed upon. In this paper we review the original genotyping schemes and discuss the basis for a novel common nomenclature for VZV viruses. We propose a minimum set of SNPs which we recommend should be used to genotype viruses. Finally, we suggest criteria by which new clades can be recognized.
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| 2. |
- Currier, Russell W, et al.
(author)
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The evolution of infectious agents in relation to sex in animals and humans: brief discussions of some individual organisms.
- 2011
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In: Annals of the New York Academy of Sciences. - : Wiley. - 1749-6632 .- 0077-8923. ; 1230, s. 74-107, s. 74-107
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Research review (peer-reviewed)abstract
- The following series of concise summaries addresses the evolution of infectious agents in relation to sex in animals and humans from the perspective of three specific questions: (1) what have we learned about the likely origin and phylogeny, up to the establishment of the infectious agent in the genital econiche, including the relative frequency of its sexual transmission; (2) what further research is needed to provide additional knowledge on some of these evolutionary aspects; and (3) what evolutionary considerations might aid in providing novel approaches to the more practical clinical and public health issues facing us currently and in the future?
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| 3. |
- Norberg, Peter, 1974, et al.
(author)
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A genome-wide comparative evolutionary analysis of herpes simplex virus type 1 and varicella zoster virus.
- 2011
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In: PloS one. - : Public Library of Science (PLoS). - 1932-6203. ; 6:7
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Journal article (peer-reviewed)abstract
- Herpes simplex virus type 1 (HSV-1) and varicella zoster virus (VZV) are closely related viruses causing lifelong infections. They are typically associated with mucocutaneous or skin lesions, but may also cause severe neurological or ophthalmic diseases, possibly due to viral- and/or host-genetic factors. Although these viruses are well characterized, genome-wide evolutionary studies have hitherto only been presented for VZV. Here, we present a genome-wide study on HSV-1. We also compared the evolutionary characteristics of HSV-1 with those for VZV. We demonstrate that, in contrast to VZV for which only a few ancient recombination events have been suggested, all HSV-1 genomes contain mosaic patterns of segments with different evolutionary origins. Thus, recombination seems to occur extremely frequent for HSV-1. We conclude by proposing a timescale for HSV-1 evolution, and by discussing putative underlying mechanisms for why these otherwise biologically similar viruses have such striking evolutionary differences.
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| 4. |
- Norberg, Peter, 1974, et al.
(author)
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Complete Nucleotide Sequence and Analysis of Two Conjugative Broad Host Range Plasmids from a Marine Microbial Biofilm
- 2014
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In: Plos One. - : Public Library of Science (PLoS). - 1932-6203. ; 9:3
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Journal article (peer-reviewed)abstract
- The complete nucleotide sequence of plasmids pMCBF1 and pMCBF6 was determined and analyzed. pMCBF1 and pMCBF6 form a novel clade within the IncP-1 plasmid family designated IncP-1 sigma. The plasmids were exogenously isolated earlier from a marine biofilm. pMCBF1 (62 689 base pairs; bp) and pMCBF6 (66 729 bp) have identical backbones, but differ in their mercury resistance transposons. pMCBF1 carries Tn5053 and pMCBF6 carries Tn5058. Both are flanked by 5 bp direct repeats, typical of replicative transposition. Both insertions are in the vicinity of a resolvase gene in the backbone, supporting the idea that both transposons are "res-site hunters'' that preferably insert close to and use external resolvase functions. The similarity of the backbones indicates recent insertion of the two transposons and the ongoing dynamics of plasmid evolution in marine biofilms. Both plasmids also carry the insertion sequence ISPst1, albeit without flanking repeats. ISPs1is located in an unusual site within the control region of the plasmid. In contrast to most known IncP-1 plasmids the pMCBF1/pMCBF6 backbone has no insert between the replication initiation gene (trfA) and the vegetative replication origin (oriV). One pMCBF1/pMCBF6 block of about 2.5 kilo bases (kb) has no similarity with known sequences in the databases. Furthermore, insertion of three genes with similarity to the multidrug efflux pump operon mexEF and a gene from the NodT family of the tripartite multi-drug resistance-nodulation-division (RND) system in Pseudomonas aeruginosa was found. They do not seem to confer antibiotic resistance to the hosts of pMCBF1/pMCBF6, but the presence of RND on promiscuous plasmids may have serious implications for the spread of antibiotic multi-resistance.
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| 5. |
- Norberg, Peter, 1974
(author)
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Divergence and genotyping of human alpha-herpesviruses: An overview.
- 2010
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In: Infection, genetics and evolution. - 1567-1348. ; 10:1, s. 14-25
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Research review (peer-reviewed)abstract
- Herpesviruses are large DNA viruses that are highly disseminated among animals. Of the eight herpesviruses identified in humans, three are classified into the α-herpesvirus subfamily: herpes simplex virus types 1 (HSV-1) and 2 (HSV-2), which are typically associated with mucocutaneous lesions, and varicella–zoster virus (VZV), which is the cause of chicken pox and herpes zoster. All three viruses establish lifelong infections and may also induce more severe symptoms, such as neurological manifestations and fatal neonatal infections. Despite thorough investigation of the genetic variability among circulating strains of each virus in recent decades, little is known about possible associations between the genetic setups of the viruses and clinical manifestations in human hosts. This review focuses mainly on evolutionary studies of and genotyping strategies for these three human α-herpesviruses, emphasizing the ambiguities induced by a high frequency of circulating recombinant strains. It also aims to shed light on the challenges of establishing a uniform genotyping strategy for all three viruses.
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| 6. |
- Norberg, Peter, 1974, et al.
(author)
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Genetic recombination of tick-borne flaviviruses among wild-type strains
- 2013
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In: Virology. - : Elsevier BV. - 0042-6822. ; 440:2, s. 105-116
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Journal article (peer-reviewed)abstract
- Genetic recombination has been suggested to occur in mosquito-borne flaviviruses. In contrast, tick-borne flaviviruses have been thought to evolve in a clonal manner, although recent studies suggest that recombination occurs also for these viruses. We re-analyzed the data and found that previous conclusions on wild type recombination were probably falsely drawn due to misalignments of nucleotide sequences, ambiguities in GenBank sequences, or different laboratory culture histories suggestive of recombination events in laboratory. To evaluate if reliable predictions of wild type recombination of tick-borne flaviviruses can be made, we analyzed viral strains sequenced exclusively for this study, and other flavivirus sequences retrieved from GenBank. We detected genetic signals supporting recombination between viruses within the three clades of TBEV-Eu, TBEV-Sib and TBEV-Fe, respectively. Our results suggest that the tick-borne encephalitis viruses may undergo recombination under natural conditions, but that geographic barriers restrict most recombination events to involve only closely genetically related viruses.
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| 7. |
- Norberg, Peter, 1974, et al.
(author)
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The IncP-1 plasmid backbone adapts to different host bacterial species and evolves through homologous recombination.
- 2011
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In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 2
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Journal article (peer-reviewed)abstract
- Plasmids are important members of the bacterial mobile gene pool, and are among the most important contributors to horizontal gene transfer between bacteria. They typically harbour a wide spectrum of host beneficial traits, such as antibiotic resistance, inserted into their backbones. Although these inserted elements have drawn considerable interest, evolutionary information about the plasmid backbones, which encode plasmid related traits, is sparse. Here we analyse 25 complete backbone genomes from the broad-host-range IncP-1 plasmid family. Phylogenetic analysis reveals seven clades, in which two plasmids that we isolated from a marine biofilm represent a novel clade. We also found that homologous recombination is a prominent feature of the plasmid backbone evolution. Analysis of genomic signatures indicates that the plasmids have adapted to different host bacterial species. Globally circulating IncP-1 plasmids hence contain mosaic structures of segments derived from several parental plasmids that have evolved in, and adapted to, different, phylogenetically very distant host bacterial species.
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| 8. |
- Tang, Ka-Wei, 1983, et al.
(author)
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Rad51 and rad52 are involved in homologous recombination of replicating herpes simplex virus DNA.
- 2014
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In: PloS one. - : Public Library of Science (PLoS). - 1932-6203. ; 9:11
-
Journal article (peer-reviewed)abstract
- Replication of herpes simplex virus 1 is coupled to recombination, but the molecular mechanisms underlying this process are poorly characterized. The role of Rad51 and Rad52 recombinases in viral recombination was examined in human fibroblast cells 1BR.3.N (wild type) and in GM16097 with replication defects caused by mutations in DNA ligase I. Intermolecular recombination between viruses, tsS and tsK, harboring genetic markers gave rise to ∼17% recombinants in both cell lines. Knock-down of Rad51 and Rad52 by siRNA reduced production of recombinants to 11% and 5%, respectively, in wild type cells and to 3% and 5%, respectively, in GM16097 cells. The results indicate a specific role for Rad51 and Rad52 in recombination of replicating herpes simplex virus 1 DNA. Mixed infections using clinical isolates with restriction enzyme polymorphisms in the US4 and US7 genes revealed recombination frequencies of 0.7%/kbp in wild type cells and 4%/kbp in GM16097 cells. Finally, tandem repeats in the US7 gene remained stable upon serial passage, indicating a high fidelity of recombination in infected cells.
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| 9. |
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| 10. |
- Ögren, Petter, 1974-, et al.
(author)
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Design and implementation of a new teleoperation control mode for differential drive UGVs
- 2014
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In: Autonomous Robots. - : Springer Science and Business Media LLC. - 0929-5593 .- 1573-7527. ; 37:1, s. 71-79
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Journal article (peer-reviewed)abstract
- In this paper, we propose and implement a new control mode for teleoperated unmanned ground vehicles (UGVs), that exploits the similarities between computer games and teleoperation robotics. Today, all teleoperated differential drive UGVs use a control mode called Tank Control, in which the UGV chassis and the pan tilt camera are controlled separately. This control mode was also the dominating choice when the computer game genre First Person Shooter (FPS) first appeared. However, the hugely successful FPS genre, including titles such as Doom, Half Life and Call of Duty, now uses a much more intuitive control mode, Free Look Control (FLC), in which rotation and translation of the character are decoupled, and controlled separately. The main contribution of this paper is that we replace Tank Control with FLC in a real UGV. Using feedback linearization, the orientation of the UGV chassis is abstracted away, and the orientation and translation of the camera are decoupled, enabling the operator to use FLC when controlling the UGV. This decoupling is then experimentally verified. The developments in the gaming community indicates that FLC is more intuitive than Tank Control and reduces the well known situational awareness problem. It furthermore reduces the need for operator training, since literary millions of future operators have already spent hundreds of hours using the interface.
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