| 1. |
- Ahlgren-Berg, Alexandra, et al.
(författare)
-
A comparative analysis of the bifunctional Cox proteins of two heteroimmune P2-like phages with different host integration sites
- 2009
-
Ingår i: Virology. - : Elsevier BV. - 0042-6822 .- 1096-0341. ; 385:2, s. 303-12
-
Tidskriftsartikel (refereegranskat)abstract
- The Cox protein of the coliphage P2 is multifunctional; it acts as a transcriptional repressor of the Pc promoter, as a transcriptional activator of the P(LL) promoter of satellite phage P4, and as a directionality factor for site-specific recombination. The Cox proteins constitute a unique group of directionality factors since they couple the developmental switch with the integration or excision of the phage genome. In this work, the DNA binding characteristics of the Cox protein of WPhi, a P2-related phage, are compared with those of P2 Cox. P2 Cox has been shown to recognize a 9 bp sequence, repeated at least 6 times in different targets. In contrast to P2 Cox, WPhi Cox binds with a strong affinity to the early control region that contains an imperfect direct repeat of 12 nucleotides. The removal of one of the repeats has drastic effects on the capacity of WPhi to bind to the Pe-Pc region. Again in contrast to P2 Cox, WPhi Cox has a lower affinity to attP compared to the Pe-Pc region, and a repeat of 9 bp can be found that has 5 bp in common with the repeat in the Pe-Pc region. WPhi Cox, however, is essential for excisive recombination in vitro. WPhi Cox, like P2 Cox, binds cooperatively with integrase to attP. Both Cox proteins induce a strong bend in their DNA targets upon binding.
|
|
| 2. |
|
|
| 3. |
- Cardoso-Palacios, Carlos, et al.
(författare)
-
A structure-function analysis of P2 integrase
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Bacteriophage P2 integrase catalyzes site-specific recombination between the phage DNA and the host chromosome thereby promoting integration or excision of the phage genome. P2 integrase belongs to the large tyrosine family of integrases that shows little sequence identity besides some conserved boxes and patches in the catalytic domain. However, the overall structure of the tyrosine family of integrases seems to be similar. Phage integrases have the potential as tools for site-specific gene insertions into eukaryotic genomes provided that target sequences are available. To elucidate the possibility of evolving the P2 integrase to accept new targets, we have in this work initiated a structure-function analysis of the P2 integrase using two approaches based on a comparison of the predicted secondary structure of P2 integrase with that determined for the lambda integrase. First, we have made hybrids between P2 integrase and the related WΦ integrase that has a different host DNA target, to locate the region promoting specificity between the integrases. This, however, has not been possible, the N-terminal domains can be exchanged without losing biological activity and this will not affect the specificity. All other hybrids made were biological inactive. Next we have made an alanine scanning of the alpha helices believed to be involved in specific interactions with the target, and four amino acids have been identified as candidates for sequence-specific interactions with the core.
|
|
| 4. |
- Cardoso-Palacios, Carlos, et al.
(författare)
-
Direct Analysis of Pharmaceutical Drugs Using Nano-DESI MS
- 2016
-
Ingår i: Journal of Analytical Methods in Chemistry. - : Hindawi Limited. - 2090-8865 .- 2090-8873.
-
Tidskriftsartikel (refereegranskat)abstract
- Counterfeit pharmaceutical drugs imply an increasing threat to the global public health. It is necessary to have systems to control the products that reach the market and to detect falsified medicines. In this work, molecules in several pharmaceutical tablets were directly analyzed using nanospray desorption electrospray ionization mass spectrometry (nano-DESI MS). Nano-DESI is an ambient surface sampling technique which enables sampling of molecules directly from the surface of the tablets without any sample pretreatment. Both the active pharmaceutical ingredients (APIs) and some excipients were detected in all analyzed tablets. Principal component analysis was used to analyze mass spectral features from different tablets showing strong clustering between tablets with different APIs. The obtained results suggest nano-DESI MS as future tool for forensic analysis to discern APIs present in unknown tablet samples.
|
|
| 5. |
|
|
| 6. |
- Cardoso Palacios, Carlos, 1970-
(författare)
-
Site-specific recombination in P2-like coliphages
- 2009
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The scope of these studies has been to investigate the site-specific recombination systems of P2-like coliphages, both in an evolutionary perspective by a comparative analysis of related phages as well as in a functional perspective. Surveys of P2-like phages in Escherichia coli isolated from nature reveal the existence of seven discrete immunity classes and three integration sites, one of them previously unknown. Phylogenetic analysis of the repressor proteins and other analyses show that homologous recombination plays a role in the appearance of new immunities. Other studies of P2-like prophages from sequenced genomes from public databases show that the P2-like phages grow in different γ-proteobacteria. Based on the type of immunity and site-specific recombination system they can be roughly subdivided in two distinct subgroups and some new host integration sites could be identified. Some of the host attachment sites have a high identity to the sequences in the human genome, making them interesting as potential tools for targeted gene insertions into unmodified human cells. The functional studies have been focused on the identification of the determinants for site specificity, which is important for the use of the enzyme for targeted gene insertions into unmodified genomes. Two approaches have been used. In one, we have performed a structure-function analysis of P2 Int that has identified several presumptive residues involved in specific binding to the core sequence, all of them located in the same alpha-helix. This knowledge could be a base for an in vitro evolution of the integrase to enable it to accept new DNA targets with a high affinity. With respect to the excisionases from P2-like coliphages integrating in different sites, we found that they share some common features when they bind and bend to their DNA targets, but there are also significant differences, especially those related to the number of binding sites and the distribution of these and the IHF binding sites in the attP regions. In the other approach we have started to characterize the site-specific recombination system of another P2-like phage, ΦD145, that has a host target with a high identity to a site in the human genome. This looks promising since the human sequence can be used in vivo in E. coli with a rather high efficiency.
|
|
| 7. |
- Hedmark, Eva, et al.
(författare)
-
Test av stängseltråden RubberGuard Wire
- 2022
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- RubberGuard Wire är en elstängseltråd som består av tunna metalltrådar överdragna med ledande gummi. Enligt distributörer kortsluts inte tråden till följd av kontakt med exempelvis vegetation och vatten. I den här studien undersökte vi hur den elektriska spänningen i stängseltråden RubberGuard Wire påverkas av kontakt med jord, vatten, mark och våt vegetation. Trådens prestanda bedömdes genom mätning av spänningen under olika förhållanden. Som jämförelse genomfördes parallella experiment med den typ av metalltråd (slät galvad High Tensile tråd (HT-tråd)) som rekommenderas till rovdjursavvisande stängsel.Experimenten visade att RubberGuard Wire påverkades på samma sätt som metalltråden vid kontakt med jord, vatten, mark och växtlighet. Vår slutsats är att RubberGuard Wire inte presterar bättre än en stängseltråd av metall när den kommer i kontakt med växande vegetation eller andra element som vanligtvis kortsluter elstängsel.
|
|
| 8. |
|
|
| 9. |
- Karlsson, Joakim L, et al.
(författare)
-
Evolution of immunity and host chromosome integration site of P2-like coliphages.
- 2006
-
Ingår i: J Bacteriol. - 0021-9193. ; 188:11, s. 3923-35
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Twenty-seven video-recorded interviews, with nine patients diagnosed with schizophrenia, were analyzed using qualitative methodology. Sequences of well- and of poorly functioning communication were distinguished, and characteristic verbal and nonverbal means of communication were described. In well functioning communication the interviewer asked short open questions, explored the emotional content in the narrative, and showed nonverbal means of communication that invited social interaction. The interviewer confirmed the patient emotionally and the narrative turned into a dialogue. The patient took a more active part and the narrative became extensive and elaborated. In poorly functioning communication the conversations were often fragmented, incoherent and confusing, with long pauses. The interviewer and the patients avoided eye-contact, and the nonverbal communication that was displayed did not accompany verbal utterances, but indicated discomfort and tension instead. Either patient or interviewer were observed dominating the conversation. In order to establish well functioning communication the interviewer’s contribution, particularly the willingness to explore and pursue the emotional content in the patient’s narrative, was found to be important.
|
|
| 10. |
- Koonjan, Shazeeda, et al.
(författare)
-
Population Dynamics of a Two Phages–One Host Infection System Using Escherichia coli Strain ECOR57 and Phages vB_EcoP_SU10 and vB_EcoD_SU57
- 2022
-
Ingår i: Pharmaceuticals. - : MDPI AG. - 1424-8247. ; 15:3
-
Tidskriftsartikel (refereegranskat)abstract
- In this study, we looked at the population dynamics of a two phages-one host system using phages vB_EcoP_SU10 (SU10) and vB_EcoD_SU57 (SU57) and the bacteria Escherichia coli, strain ECOR57. Phage-specific growth curves were observed where infections by SU10 resulted in a moderate production of phages and infections by SU57 resulted in a fast and extensive production of phage progeny. Sequentially adding SU10 followed by SU57 did not produce a significant change in growth rates, whereas adding SU57 followed by SU10 resulted in a decrease in SU10 titer The efficiency of the plating assays showed that ECOR57 exhibited a resistance spectrum after infection by both the single and combined phages. Phage-resistant bacteria exhibited four different morphotypes (i.e., normal, slimy, edgy, and pointy). The normal and edgy morphotypes had a high frequency of developing resistance. Bacterial growth and biofilm assays indicated that the edgy and pointy morphotypes reached a stationary phase faster and produced more biofilm compared to the wild type. These findings suggest that the dynamic structure of phage–bacteria communities dictate resistance evolution and development. Understanding when and how resistances arise and phage(s)–hosts interactions could aid in the design of phage therapy treatments.
|
|
| 11. |
- Li, Xiaoze, et al.
(författare)
-
Eight Nucleotide Substitutions Inhibit Splicing to HPV-16 3'-Splice Site SA3358 and Reduce the Efficiency by which HPV-16 Increases the Life Span of Primary Human Keratinocytes.
- 2013
-
Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:9
-
Tidskriftsartikel (refereegranskat)abstract
- The most commonly used 3'-splice site on the human papillomavirus type 16 (HPV-16) genome named SA3358 is used to produce HPV-16 early mRNAs encoding E4, E5, E6 and E7, and late mRNAs encoding L1 and L2. We have previously shown that SA3358 is suboptimal and is totally dependent on a downstream splicing enhancer containingmultiple potential ASF/SF2 binding sites. Here weshow that only one of the predicted ASF/SF2 sites accounts for the majority of the enhancer activity. We demonstrate that single nucleotide substitutions in this predicted ASF/SF2 site impair enhancer function and that this correlates with less efficient binding to ASF/SF2 in vitro. We provide evidence that HPV-16 mRNAs that arespliced to SA3358 interact with ASF/SF2 in living cells. In addition,mutational inactivation of the ASF/SF2 site weakened the enhancer at SA3358 in episomal forms of the HPV-16 genome, indicating that the enhancer is active in the context of the full HPV-16 genome.This resulted in induction of HPV-16 late gene expression as a result of competition from late splice site SA5639. Furthermore, inactivation of the ASF/SF2 site of the SA3358 splicing enhancer reduced the ability of E6- and E7-encoding HPV-16 plasmids to increase the life span of primary keratinocytes in vitro, demonstrating arequirement for an intact splicing enhancer of SA3358 forefficient production of the E6 and E7 mRNAs. These results link the strength of the HPV-16 SA3358 splicing enhancer to expression of E6 and E7 and to the pathogenic properties of HPV-16.
|
|
| 12. |
- Mandali, Sridhar, et al.
(författare)
-
Characterization of the site-specific recombination system of phage ΦD145, and its capacity to promote recombination in human cells
- 2010
-
Ingår i: Virology. - : Elsevier BV. - 0042-6822 .- 1096-0341. ; 408:1, s. 64-70
-
Tidskriftsartikel (refereegranskat)abstract
- Phage integrases have the potential of becoming tools for safe site-specific integration of genes into unmodified human genomes. The P2-like phages have been found to have different bacterial host integration sites and consequently they have related integrases with different sequence specificities. In this work the site-specific recombination system of the P2-like phage ΦD145 is characterized. The minimal attB site is determined to 22 nt with 18 nt identity to the core region of attP. A non-coding sequence on the human chromosome 13 is shown to be a rather good substrate for recombination in vivo in bacteria as well as in a plasmid system in HeLa cells when HMG protein recognition sequences are inserted between the left arm-binding site and the core in the complex phage attachment site attP. Thus ΦD145 integrase that belongs to the tyrosine family shows potential as a tool for site-specific integration into the human genome.
|
|
| 13. |
- Månsson, Johan, et al.
(författare)
-
Sångsvan på jordbruksmark – prefererade grödor, skador och skrämsel
- 2022
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Med en växande population av sångsvan i Sverige och Europa finns det behov av mer kunskap om de skador de kan orsaka på växande gröda.Vår genomgång av litteratur visar, liksom tidigare litteraturgenomgångar, att det generellt finns få studier tillgängliga som studerat vilka grödor svanarna väljer och hur deras bete på grödor påverkar skördeutfallet.Vår genomgång av tidigare vetenskaplig litteratur och viltskadestatistik visar att sångsvan i stor utsträckning betar och skadar raps och spannmål som korn och vete.Även antalet studier kring effekter av skrämsel av sångsvan är ytterst begränsat. Vi utförde en pilotstudie för att se om sångsvanarna beteende skiljer sig mot grågäss när de blir utsatta för skrämsel. Vi kunde inte se någon skillnad mellan sångsvan och gäss för det avstånd de lyfter när en människa närmar sig fåglarna. Det tyder på att den kunskap som finns tillgänglig för de mer välstuderade gässen i viss mån går att överföra på sångsvan. Man ska dock vara försiktig med att generalisera våra resultat, eftersom studien var begränsad i både tid (vinter) och rum (enbart Skåne).
|
|
| 14. |
- Nilsson, Hanna, et al.
(författare)
-
Phylogenetic structure and evolution of regulatory genes and integrases of P2-like phages
- 2011
-
Ingår i: Bacteriophage. - Austin, Texas, USA : Landes Bioscience. - 2159-7073 .- 2159-7081. ; 1:4, s. 207-218
-
Tidskriftsartikel (refereegranskat)abstract
- The phylogenetic relationships and structural similarities of the proteins encoded within the regulatory region (containing the integrase gene and the lytic – lysogenic transcriptional switch genes) of P2-like phages were analyzed, and compared to the phylogenetic relationship of P2-like phages inferred from four structural genes. P2-like phages are thought to be one of the most genetically homogenous phage groups but the regulatory region nevertheless varies extensively between different phage genomes. The analyses showed that there are many types of regulatory regions, but two types can be clearly distinguished; regions similar either to the phage P2 or to the phage 186 regulatory regions. These regions were also found to be most frequent among the sequenced P2-like phage or prophage genomes, and common in phages using Escherichia coli as a host. Both the phylogenetic and the structural analyses showed that these two regions are related. The integrases as well as the cox/apl genes show a common monophyletic origin but the immunity repressor genes, the type P2 C gene and the type 186 cI gene, are likely of different origin. There was no indication of recombination between the P2 – 186 types of regulatory genes but the comparison of the phylogenies of the regulatory region with the phylogeny based on four structural genes revealed recombinational events between the regulatory region and the structural genes. Less common regulatory regions were phylogenetically heterogeneous and typically contained a fusion of genes from distantly related or unknown phages and P2-like genes.
|
|
| 15. |
- Svensson, Linn, et al.
(författare)
-
Inventering av varg vintern 2020–2021
- 2021
-
Rapport (populärvet., debatt m.m.)abstract
- Mål och metodik Vargstammen i Sverige och Norge utgör en gemensam skandinavisk population med utbredning över riksgränsen. Årliga inventeringar ska genomföras vintertid i respektive land enligt överenskommen gemensam inventeringsmetodik. Utbredning, utveckling och storlek på vargstammen dokumenteras genom kartläggning av antal vargrevir med familjegrupper, revirmarkerande par samt föryngringar under inventeringsperioden 1 oktober – 31 mars. Antal vargindivider i Skandinavien beräknas med samma metod som föregående vinter med en omräkningsfaktor från antal bekräftade valpkullar (föryngringar) till antal individer (antal föryngringar multipliceras med 10).Inventeringen genomförs i huvudsak genom spårning på snö samt DNA-analyser av spillning, urin och hår. Information från radiotelemetri, forskningsdata samt döda vargar används när sådan information finns tillgänglig. Länsstyrelserna i Sverige och SNO (Statens Naturoppsyn) i samarbete med Høgskolen i Innlandet i Norge är ansvariga för att genomföra inventeringen i fält. De kontrollerar även i fält de rapporter om spår och andra observationer som allmänheten i stor utsträckning bidrar med under inventeringsarbetet.Antal familjegrupper och revirmarkerande parUnder inventeringsperioden 2020-2021 dokumenterades 48 familjegrupper i Skandinavien, varav 36 i Sverige, fem i Norge och sju gränsrevir, d.v.s belägna över den svensk-norska riksgränsen. Totalt dokumenterades 27 revirmarkerande par varav 21 i Sverige, fem i Norge och ett gränsrevir. Efter fördelning av de totalt åtta gränsreviren med hälften av varje revir till respektive land summeras för Sverige 39,5 familjegrupper och 21,5 revirmarkerande par. För Norge blir motsvarande summa 8,5 familjegrupper och 5,5 revirmarkerande par.Antal föryngringarUnder inventeringsperioden dokumenterades 48 föryngringar (valpkullar) av varg i Skandinavien varav 36 föryngringar i helsvenska revir, fem i helnorska revir och sju i revir som var belägna på gränsen mellan Sverige och Norge.PopulationsuppskattningMed samma metod som användes förra säsongen (antal föryngringar multipliceras med 10), beräknas den skandinaviska populationen till 480 vargar (95% CI = 379-624). Den svenska delen av populationen, med halva gränsrevir inkluderade, beräknas med samma metod till 395 (95% CI = 312-513) vargar. Metoden baseras på antal dokumenterade föryngringar och inkluderar levande samt kända döda vargar under hela inventeringsperioden 1 oktober – 31 mars. I den norska populationen dokumenterades 83-86 vargar varav 57-58 helnorska vargar samt hälften av de 52- 56 vargar som dokumenterats på båda sidor riksgränsen.GenetikTvå sedan tidigare kända finsk-ryska vargar var fortsatt stationära i populationens reproduktionsområde. En tik i en familjegrupp i Sverige och en hane i ett revirmarkerande par i Norge. Ingen av dem fick valpar våren 2020, och det norska paret flyttades av förvaltningen längre söderut i Norge. Tre nya finsk-ryska vargar dokumenterades i norra Sverige, två av dem fälldes vid skyddsjakt i renskötselområdet under hösten och vintern 2020. Den tredje vargen dokumenterades vid några olika tillfällen i Norrbottens län under vintern. Därtill påvisades 11 F1:or, efter tre kända finsk-ryska vargar, som revirhävdande djur i revirmarkerande par eller familjegrupper.Den genomsnittliga inavelskoefficienten som uppskattar inavelsnivån i populationen har beräknats till 0,23 (±0,09 SD) för vinterns familjegrupper, vilket är en svag minskning jämfört med förra säsongen (0,24 ±0,09 SD).
|
|
