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- Ho, Joshua W. K., et al.
(författare)
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Comparative analysis of metazoan chromatin organization
- 2014
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 512:7515, s. 449-U507
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Tidskriftsartikel (refereegranskat)abstract
- Genome function is dynamically regulated in part by chromatin, which consists of the histones, non-histone proteins and RNA molecules that package DNA. Studies in Caenorhabditis elegans and Drosophila melanogaster have contributed substantially to our understanding of molecular mechanisms of genome function in humans, and have revealed conservation of chromatin components and mechanisms(1-3). Nevertheless, the three organisms have markedly different genome sizes, chromosome architecture and gene organization. On human and fly chromosomes, for example, pericentric heterochromatin flanks single centromeres, whereas worm chromosomes have dispersed heterochromatin-like regions enriched in the distal chromosomal 'arms', and centromeres distributed along their lengths(4,5). To systematically investigate chromatin organization and associated gene regulation across species, we generated and analysed a large collection of genome-wide chromatin data sets from cell lines and developmental stages in worm, fly and human. Here we present over 800 new data sets from our ENCODE and modENCODE consortia, bringing the total to over 1,400. Comparison of combinatorial patterns of histone modifications, nuclear lamina-associated domains, organization of large-scale topological domains, chromatin environment at promoters and enhancers, nucleosome positioning, and DNA replication patterns reveals many conserved features of chromatin organization among the three organisms. We also find notable differences in the composition and locations of repressive chromatin. These data sets and analyses provide a rich resource for comparative and species-specific investigations of chromatin composition, organization and function.
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| 2. |
- Kaden, René, 1975-, et al.
(författare)
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A novel real-time PCR assay for specific detection of Brucella melitensis
- 2017
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Ingår i: BMC Infectious Diseases. - : BIOMED CENTRAL LTD. - 1471-2334. ; 17
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Tidskriftsartikel (refereegranskat)abstract
- Background: Brucellosis is a zoonosis that occurs worldwide. The disease has been completely eradicated in livestock in Sweden in 1994, and all cases of confirmed human brucellosis are imported into Sweden from other countries. However, due to an increase in the number of refugees and asylum seekers from the middle-east to Sweden, there is a need to improve the current diagnostic methodology for Brucella melitensis. Whilst culture of Brucella species can be used as a diagnostic tool, real-time PCR approaches provide a much faster result. The aim of this study was to set up a species-specific real-time PCR for the detection of all biovars of Brucella melitensis, which could be used routinely in diagnostic laboratories. Methods: A Brucella melitensis real-time PCR assay was designed using all available genomes in the public database of Brucella (N=96) including all complete genomes of Brucella melitensis (N=17). The assay was validated with a collection of 37 Brucella species reference strains, 120 Brucella melitensis human clinical isolates, and 45 clinically relevant non-Brucella melitensis strains. Results: In this study we developed a single real-time PCR for the specific detection of all biovars of Brucella melitensis. Conclusions: This new real-time PCR method shows a high specificity (100%) and a high sensitivity ( 1.25 GE/mu l) and has been implemented in the laboratories of four governmental authorities across Sweden.
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| 3. |
- Kaden, Rene, 1975-, et al.
(författare)
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Brucella abortus : determination of survival times and evaluation of methods for detection in several matrices
- 2018
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Ingår i: BMC Infectious Diseases. - : Springer Science and Business Media LLC. - 1471-2334. ; 18
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Brucella abortus is a highly pathogenic zoonotic agent, tempting for the development of a rapid diagnostic method to enable adequate treatment and prevent further spread. Enrichment of the bacteria is often used as a first step in diagnostics to increase the bacterial number above the detection limit of the real-time PCR. The enrichment of Brucella spp. takes at least 3 days, which might be avoidable if sensitive PCR methods can be used. Since many matrices contain PCR inhibitors, the limit of detection (LOD) must be determined for each separate matrix. Another aim of this study was the determination of survival of Brucella abortus in the analyzed matrices. METHODS: The LOD for the detection of B. abortus in 14 matrices, relevant for human medicine, veterinary medicine and food and feed safety, was determined to evaluate the need of a pre-enrichment step prior to real-time PCR. The survival of B. abortus in the spiked matrices was tested by plate count in a 7-day interval for 132 days. RESULTS: The limit of detection for B. abortus in most matrices was in the range of 10(3)-10(4) CFU/g for cultivation and 10(4)-10(5) CFU/g for direct real-time PCR. The survival time of B. abortus was less than 21 days in apple puree and stomach content and 28 days in water while B. abortus remained viable at day 132 in milk, blood, spinach and minced meat. CONCLUSIONS: A direct PCR analysis without enrichment of bacteria saves at least 3 days. However, the limit of detection between direct PCR and plate count differs in a 10 fold range. We conclude that this lower sensitivity is acceptable in most cases especially if quick analysis are required.
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| 4. |
- Kaden, Rene, et al.
(författare)
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Brucellosis outbreak in a Swedish kennel in 2013 : Determination of genetic markers for source tracing
- 2014
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Ingår i: Veterinary Microbiology. - : Elsevier BV. - 0378-1135 .- 1873-2542. ; 174:3–4, s. 523-530
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Tidskriftsartikel (refereegranskat)abstract
- Brucellosis is a highly infectious zoonotic disease but rare in Sweden. Nonetheless, an outbreak of canine brucellosis caused by an infected dog imported to Sweden was verified in 2013. In total 25 dogs were tested at least duplicated by the following approaches: real-time PCR for the detection of Brucella canis, a Brucella genus-specific real-time PCR, selective cultivation, and microscopic examination. The whole genome of B. canis strain SVA13 was analysed regarding genetic markers for epidemiological examination. The genome of an intact prophage of Roseobacter was detected in B. canis strain SVA13 with whole genome sequence prophage analysis (WGS-PA). It was shown that the prophage gene content in the American, African and European isolates differs remarkably from the Asian strains. The prophage sequences in Brucella may therefore serve of use as genetic markers in epidemiological investigations. Phage DNA fragments were also detected in clustered, regularly interspaced short palindromic repeats (CRISPR) in the genome of strain SVA13. In addition to the recommendations for genetic markers in Brucella outbreak tracing, our paper reports a validated two-step stand-alone real-time PCR for the detection of B. canis and its first successful use in an outbreak investigation.
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| 7. |
- Wahab, Tara, et al.
(författare)
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Draft Genome Sequences of Brucella suis Biovar 4 Strain NCTC 10385, Brucella ceti Strain NCTC 12891T, Brucella inopinata Strain CAMP 6436T, and Brucella neotomae Strain ATCC 23459T
- 2014
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Ingår i: Genome Announcements. - 2169-8287. ; 2:5, s. e00783-14-
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Tidskriftsartikel (refereegranskat)abstract
- With the aim of developing quantitative PCR methods for the detection and differentiation of Brucella species, the genomes of Brucella ceti, Brucella inopinata, Brucella netotomae, and Brucella suis biovar 4 were sequenced and analyzed.
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