| 1. |
- Bell, Jane C., et al.
(författare)
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Survival of infants born with esophageal atresia among 24 international birth defects surveillance programs
- 2021
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Ingår i: Birth Defects Research. - : Wiley. - 2472-1727. ; 113:12, s. 945-957
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Tidskriftsartikel (refereegranskat)abstract
- Background: Esophageal atresia (EA) affects around 2.3–2.6 per 10,000 births world-wide. Infants born with this condition require surgical correction soon after birth. Most survival studies of infants with EA are locally or regionally based. We aimed to describe survival across multiple world regions. Methods: We included infants diagnosed with EA between 1980 and 2015 from 24 birth defects surveillance programs that are members of the International Clearinghouse for Birth Defects Surveillance and Research. We calculated survival as the proportion of liveborn infants alive at 1 month, 1- and 5-years, among all infants with EA, those with isolated EA, those with EA and additional anomalies or EA and a chromosomal anomaly or genetic syndrome. We also investigated trends in survival over the decades, 1980s–2010s. Results: We included 6,466 liveborn infants with EA. Survival was 89.4% (95% CI 88.1–90.5) at 1-month, 84.5% (95% CI 83.0–85.9) at 1-year and 82.7% (95% CI 81.2–84.2) at 5-years. One-month survival for infants with isolated EA (97.1%) was higher than for infants with additional anomalies (89.7%) or infants with chromosomal or genetic syndrome diagnoses (57.3%) with little change at 1- and 5-years. Survival at 1 month improved from the 1980s to the 2010s, by 6.5% for infants with isolated EA and by 21.5% for infants with EA and additional anomalies. Conclusions: Almost all infants with isolated EA survived to 5 years. Mortality was higher for infants with EA and an additional anomaly, including chromosomal or genetic syndromes. Survival improved from the 1980s, particularly for those with additional anomalies.
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| 2. |
- Christerson, Linus, 1985-, et al.
(författare)
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High-Resolution Genotyping of Chlamydia trachomatis by Use of a Novel Multilocus Typing DNA Microarray
- 2011
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Ingår i: Journal of Clinical Microbiology. - 0095-1137 .- 1098-660X. ; 49:8, s. 2838-2843
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Tidskriftsartikel (refereegranskat)abstract
- Typing of Chlamydia trachomatis is important to understandingits epidemiology. Currently used methods such as DNA sequencingof the ompA gene and multilocus sequence typing (MLST) eitheroffer limited epidemiological resolution or are laborious andexpensive, or both. DNA microarray technology using the ArrayStripformat is an affordable alternative for genotyping. In thisstudy, we developed a new multilocus typing (MLT) DNA microarray,based on the target regions of a high-resolution MLST systemas well as software for easy analysis. Validation of the arraywas done by typing 80 previously MLST-typed clinical specimensfrom unselected adolescents in school. The MLT array showed100% specificity and provided 2.4-times-higher resolution thanompA sequencing, separating the commonly predominating ompAE/Bour genotype into 7 MLT array genotypes. The MLT array reproducedepidemiological findings revealed by the MLST system and showedsufficient sensitivity to work with clinical specimens. Comparedto MLST analysis, the expenses needed for testing a sample withthe MLT array are considerably lower. Moreover, testing canbe completed within 1 working day rather than 3 or 4 days, withdata analysis not requiring highly specialized personnel. Thepresent MLT array represents a powerful alternative in C. trachomatisgenotyping.
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| 3. |
- Isaksson, Jenny, et al.
(författare)
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Comparison of multilocus sequence typing and multilocus typing microarray of Chlamydia trachomatis strains from Argentina and Chile
- 2016
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Ingår i: Journal of Microbiological Methods. - : Elsevier BV. - 0167-7012 .- 1872-8359. ; 127, s. 214-218
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Tidskriftsartikel (refereegranskat)abstract
- This study compared conventional ompA genotyping of Chlamydia trachomatis with multilocus sequence typing (MLST) and multilocus typing (MLT) DNA microarray. DNA extracts of 104 C trachomatis positive specimens were analyzed by ompA sequencing and MIST and of these 76 by MLT array. Obtained MIST sequence types (STs) were compared to sequences in the database http://mIstdb.uu.se. The resolution obtained for MIST (35 STs) was 2.1 higher than for ompA sequencing (17 variants) and 13 higher than MLT array (27 MLT groups). Among the 104 samples the predominant genotype E could be divided into 5 ompA variants and 23 STs of which 16 had not been reported in previous studies. The most common STs, ST3 and ST56, were identified as founders and are common in several countries on a global scale. The MIST and the MLT array provided similar strain discrimination capacity and showed considerably higher resolution than conventional ompA sequencing.
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| 4. |
- Konrad, Anke, et al.
(författare)
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The evolution of catalytic residues and enzyme mechanism within the bacterial nucleoside phosphorylase superfamily 1
- 2012
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Ingår i: Gene. - : Elsevier BV. - 1879-0038 .- 0378-1119. ; 510:2, s. 154-161
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Tidskriftsartikel (refereegranskat)abstract
- Nucleoside phosphorylases are essential for the salvage and catabolism of nucleotides in bacteria and other organisms, and members of this enzyme superfamily have been of interest for the development of antimicrobial and cancer therapies. The nucleotide phosphorylase superfamily 1 encompasses a number of different enzymes which share a general superfold and catalytic mechanism, while they differ in the nature of the nucleophiles used and in the nature of characteristic active site residues. Recently, one subfamily, the uridine phosphorylases, has been subdivided into two types which differ with respect to the mechanism of transition state stabilization, as dictated by differences in critical amino acid residues. Little is known about the phylogenetic distribution and relationship of the two different types, as well as the relationship to other NP-1 superfamily members. Here comparative genomic analysis illustrates that UP-Is and UP-2s fall into monophyletic groups and are biased with respect to species representation. UP-1 evolved in Gram negative bacteria, while Gram positive species tend to predominantly contain UP-2. PNP (a sister clade to all UPs) contains both Gram positive and Gram negative species. The findings imply that the nucleoside phosphorylase superfamily I evolved through a series of three important duplications, leading to the separate, monophyletic enzyme families, coupled to individual lateral transfer events. Extensive horizontal transfer explains the occurrence of unexpected uridine phosphorylases in some genomes. This study provides a basis for understanding the evolution of uridine and purine nucleoside phosphorylases with respect to DNA/RNA metabolism and with potential utility in the design of antimicrobial and anti-tumor drugs. (C) 2012 Elsevier B.V. All rights reserved.
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| 5. |
- Konrad, Anke, et al.
(författare)
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The global distribution and evolution of deoxyribonucleoside kinases in bacteria
- 2012
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Ingår i: Gene. - : Elsevier BV. - 1879-0038 .- 0378-1119. ; 492:1, s. 117-120
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Tidskriftsartikel (refereegranskat)abstract
- Deoxyribonucleoside kinases (dNKs) are important to DNA metabolism, especially in environments where nucleosides are freely available to be absorbed and used for the salvage pathway. Little has previously been known about the complement of dNKs in different bacterial genomes. However, it was believed that Gram-negative bacteria had a single dNK, while Gram-positive bacteria possessed several. An analysis of 992 fully sequenced bacterial genomes, including both Gram-positive and Gram-negative organisms, was conducted to investigate the phylogenetic relationship of all TK1-like and non-TK1-like dNKs. It was illustrated that both gene families evolved through a number of duplications and horizontal gene transfers, leading to the presence of multiple dNKs in different types of bacteria. The findings of this study provide a backbone for further studies into the evolution of the interplay between the de novo and salvage pathways in DNA synthesis with respect to environmental availability of deoxyribonucleosides and metabolic processes generating the provisions of different dNTPs. (C) 2011 Elsevier B.V. All rights reserved.
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| 6. |
- Konrad, Anke, et al.
(författare)
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The Phylogenetic Distribution and Evolution of Enzymes Within the Thymidine Kinase 2-like Gene Family in Metazoa
- 2014
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Ingår i: Journal of Molecular Evolution. - : Springer Science and Business Media LLC. - 0022-2844 .- 1432-1432. ; 78:3-4, s. 202-216
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Tidskriftsartikel (refereegranskat)abstract
- Deoxyribonucleoside kinases (dNKs) carry out the rate-determining step in the nucleoside salvage pathway within all domains of life where the pathway is present, and, hence, are an indication on whether or not a species/genus retains the ability to salvage deoxyribonucleosides. Here, a phylogenetic tree is constructed for the thymidine kinase 2-like dNK gene family in metazoa. Each enzyme class (deoxycytidine, deoxyguanosine, and deoxythymidine kinases, as well as the multisubstrate dNKs) falls into a monophyletic clade. However, in vertebrates, dCK contains an apparent duplication with one paralog lost in mammals, and a number of crustacean genomes (like Caligus rogercresseyi and Lepeophtheirus salmonis) unexpectedly contain not only the multisubstrate dNKs, related to Drosophila multisubstrate dNK, but also a TK2-like kinase. Additionally, crustaceans (Daphnia, Caligus, and Lepeophtheirus) and some insects (Tribolium, Danaus, Pediculus, and Acyrthosiphon) contain several multisubstrate dNK-like enzymes which group paraphyletically within the arthropod clade. This might suggest that the multisubstrate dNKs underwent multiple rounds of duplications with differential retention of duplicate copies between insect families and more complete retention within some crustaceans and insects. Genomes of several basal animalia contain more than one dNK-like sequence, some of which group outside the remaining eukaryotes (both plants and animals) and/or with bacterial dNKs. Within the vertebrates, the mammalian genomes do not contain the second dCK, while birds, fish, and amphibians do retain it. Phasianidae (chicken and turkey) have lost dGK, while it has been retained in other bird lineages, like zebra finch. Reconstruction of the ancestral sequence between the multisubstrate arthropod dNKs and the TK2 clade of vertebrates followed by homology modeling and discrete molecular dynamics calculations on this sequence were performed to examine the evolutionary path which led to the two different enzyme classes. The structural models showed that the carboxyl terminus of the ancestral sequence is more helical than dNK, in common with TK2, although any implications of this for enzyme specificity will require biochemical validation. Finally, rate-shift and conservation-shift analysis between clades with different specificities uncovered candidate residues outside the active site pocket which may have contributed to differentiation in substrate specificity between enzyme clades.
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| 7. |
- Ruettger, Anke, et al.
(författare)
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Genotyping of Chlamydia trachomatis strains from culture and clinical samples using an ompA-based DNA microarray assay
- 2011
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Ingår i: Molecular and Cellular Probes. - : Elsevier BV. - 0890-8508 .- 1096-1194. ; 25:1, s. 19-27
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Tidskriftsartikel (refereegranskat)abstract
- Current typing methods of Chlamydia (C) trachomatis are mainly based on the diversity of the ompA gene, which is coding for the major outer membrane protein A. The present study aimed at facilitating genotyping of strains of this obligate intracellular human pathogen by developing a DNA microarray assay using the ArrayTube (TM) format for individual samples and the ArrayStrip (TM) format for higher throughput. The new test is exploiting multiple discriminatory sites by involving a total of 61 oligonucleotide probes representing genotype-specific polymorphisms in variable domains 1, 2 and 4 of the ompA gene. After multiplex amplification of these domains using biotinylated primers, the sample is hybridized in the microarray vessel under highly stringent conditions. The resulting binding pattern is genotype specific, thus allowing direct identification. We were able to show that DNA from each of the currently accepted genotypes (serovars) yielded a unique, theoretically expected and distinct hybridization pattern. The assay was also shown to be highly sensitive as a dilution containing the equivalent of 1 inclusion-forming unit was still correctly genotyped. In addition, when 62 clinical samples were examined and compared to PCR-RFLP typing results, the genotype was correctly identified by the DNA microarray in all cases. The present test is easy to handle and economically affordable, and it allows genotyping of C. trachomatis to be accomplished within a working day, thus lending itself for epidemiological studies and routine diagnosis.
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| 8. |
- Tinta, Tinkara, et al.
(författare)
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Deoxyribonucleoside kinases in two aquatic bacteria with high specificity for thymidine and deoxyadenosine.
- 2012
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Ingår i: FEMS Microbiology Letters. - : Oxford University Press (OUP). - 1574-6968 .- 0378-1097. ; 331:2, s. 120-127
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Tidskriftsartikel (refereegranskat)abstract
- Deoxyribonucleoside kinases (dNKs) are essential in the mammalian cell but their 'importance' in bacteria, especially aquatic ones, is less clear. We studied two aquatic bacteria, Gram-negative Flavobacterium psychrophilum JIP02/86 and Polaribacter sp. MED152, for their ability to salvage deoxyribonucleosides (dNs). Both had a Gram-positive-type thymidine kinase (TK1), which could phosphorylate thymidine, and one non-TK1 dNK, which could efficiently phosphorylate deoxyadenosine and slightly also deoxycytosine. Surprisingly, the four tested dNKs could not phosphorylate deoxyguanosine, and apparently, these two bacteria are missing this activity. When tens of available aquatic bacteria genomes were examined for the presence of dNKs, a majority had at least a TK1-like gene, but several lacked any dNKs. Apparently, among aquatic bacteria, the role of the dN salvage varies.
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| 9. |
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| 10. |
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