| 11. |
- Geny, Sylvain, et al.
(författare)
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Next-generation bis-locked nucleic acids with stacking linker and 2 '-glycylamino-LNA show enhanced DNA invasion into supercoiled duplexes
- 2016
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 44:5, s. 2007-2019
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Tidskriftsartikel (refereegranskat)abstract
- Targeting and invading double-stranded DNA with synthetic oligonucleotides under physiological conditions remain a challenge. Bis-locked nucleic acids (bisLNAs) are clamp-forming oligonucleotides able to invade into supercoiled DNA via combined Hoogsteen and Watson-Crick binding. To improve the bisLNA design, we investigated its mechanism of binding. Our results suggest that bisLNAs bind via Hoogsteen-arm first, followed by Watson-Crick arm invasion, initiated at the tail. Based on this proposed hybridization mechanism, we designed next-generation bisLNAs with a novel linker able to stack to adjacent nucleobases, a new strategy previously not applied for any type of clamp-constructs. Although the Hoogsteen-arm limits the invasion, upon incorporation of the stacking linker, bisLNA invasion is significantly more efficient than for non-clamp, or nucleotide-linker containing LNA-constructs. Further improvements were obtained by substituting LNA with 2'-glycylamino-LNA, contributing a positive charge. For regular bisLNAs a 14-nt tail significantly enhances invasion. However, when two stacking linkers were incorporated, tail-less bisLNAs were able to efficiently invade. Finally, successful targeting of plasmids inside bacteria clearly demonstrates that strand invasion can take place in a biologically relevant context.
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| 12. |
- Gros Calvo, Meritxell, et al.
(författare)
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Pharmaceuticals in source separated sanitation systems : Fecal sludge and blackwater treatment
- 2019
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Ingår i: Science of the Total Environment. - : Elsevier B.V.. - 0048-9697 .- 1879-1026.
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Tidskriftsartikel (refereegranskat)abstract
- This study investigated, for the first time, the occurrence and fate of 29 multiple-class pharmaceuticals (PhACs) in two source separated sanitation systems based on: (i) batch experiments for the anaerobic digestion (AD) of fecal sludge under mesophilic (37 °C) and thermophilic (52 °C) conditions, and (ii) a full-scale blackwater treatment plant using wet composting and sanitation with urea addition. Results revealed high concentrations of PhACs in raw fecal sludge and blackwater samples, with concentrations up to hundreds of μg L−1 and μg kg−1 dry weight (dw) in liquid and solid fractions, respectively. For mesophilic and thermophilic treatments in the batch experiments, average PhACs removal rates of 31% and 45%, respectively, were observed. The average removal efficiency was slightly better for the full-scale blackwater treatment, with 49% average removal, and few compounds, such as atenolol, valsartan and hydrochlorothiazide, showed almost complete degradation. In the AD treatments, no significant differences were observed between mesophilic and thermophilic conditions. For the full-scale blackwater treatment, the aerobic wet composting step proved to be the most efficient in PhACs reduction, while urea addition had an almost negligible effect for most PhACs, except for citalopram, venlafaxine, oxazepam, valsartan and atorvastatin, for which minor reductions (on average 25%) were observed. Even though both treatment systems reduced initial PhACs loads considerably, significant PhAC concentrations remained in the treated effluents, indicating that fecal sludge and blackwater fertilizations could be a relevant vector for dissemination of PhACs into agricultural fields and thus the environment.
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| 13. |
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| 14. |
- Helgadottir, Hafdis, et al.
(författare)
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Somatic mutation that affects transcription factor binding upstream of CD55 in the temporal cortex of a late-onset Alzheimer disease patient
- 2019
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 28:16, s. 2675-2685
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Tidskriftsartikel (refereegranskat)abstract
- Alzheimer's disease (AD) is the most common neurodegenerative disease worldwide. Familial cases suggest genetic components; however, monogenetic causes are few, and the vast majority of incidences have unknown cause. Sequencing efforts have focused on germline mutations, but improved technology has opened up for studies on somatic mutations in affected brain tissue samples. Here we use ultra-deep sequencing on brain and blood from early-onset AD (EOAD) and late-onset AD (LOAD) patients and non-AD individuals (n = 16). In total, 2.86 Mb of genomic regions, previously associated with AD, were targeted included 28 genes and upstream and downstream regulatory regions. Tailored downstream bioinformatics filtering identified 11 somatic single nucleotide variants in the temporal cortex in AD patients and none in the controls. One variant was validated to be present at 0.4% allele frequency in temporal cortex of a LOAD patient. This variant was predicted to affect transcription factor binding sites upstream of the CD55 gene, contributing to AD pathogenesis by affecting the complement system. Our results suggest that future studies targeting larger portions of the genome for somatic mutation analysis are important to obtain an increased understanding for the molecular basis of both EOAD and LOAD.
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| 15. |
- Josefsson, Sarah, et al.
(författare)
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Persistent Organic Pollutants in Streamwater : Influence of Hydrological Conditions and Landscape Type
- 2016
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 50:14, s. 7416-7424
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Tidskriftsartikel (refereegranskat)abstract
- Concentrations of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), polychlorinated biphenyls (PCBs), and hexachlorobenzene (HCB) in streamwater were measured in a remote catchment in northern Sweden and downstream to the Baltic Sea. Sampling took place at seven sites during two years and under different hydrological conditions: during the snow-free, snow-covered, and spring-flood seasons. Concentrations varied substantially between seasons and were up to 20 times higher during the spring flood compared to the preceding snow-covered period. The increase in concentrations with runoff was due to higher levels of particle-associated contaminants, while the dissolved concentrations remained stable. Particulate-contaminant concentrations were positively correlated primarily to suspended particulate matter (SPM) at sites in areas with a high land-cover fraction of sorted sediment. When upstream sampling locations were compared, a mire-dominated stream had higher concentrations and a lower retention of atmospherically deposited contaminants than a forest stream of the same catchment size. Contaminant concentrations (normalized to volume) did not increase consistently downstream despite the presence of several point sources. However, when normalized to the amount of SPM, concentrations were on average >20 times higher at the outlet in the Baltic Sea compared to the outlet from the remote catchment without point sources.
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| 16. |
- Kaaks, Rudolf, et al.
(författare)
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Tumor-associated autoantibodies as early detection markers for ovarian cancer? : A prospective evaluation
- 2018
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Ingår i: International Journal of Cancer. - : Wiley-Blackwell. - 0020-7136 .- 1097-0215. ; 143:3, s. 515-526
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Tidskriftsartikel (refereegranskat)abstract
- Immuno-proteomic screening has identified several tumor-associated autoantibodies (AAb) that may have diagnostic capacity for invasive epithelial ovarian cancer, with AAbs to P53 proteins and cancer-testis antigens (CTAGs) as prominent examples. However, the early detection potential of these AAbs has been insufficiently explored in prospective studies. We performed ELISA measurements of AAbs to CTAG1A, CTAG2, P53 and NUDT11 proteins, for 194 patients with ovarian cancer and 705 matched controls from the European EPIC cohort, using serum samples collected up to 36 months prior to diagnosis under usual care. CA125 was measured using electrochemo-luminiscence. Diagnostic discrimination statistics were calculated by strata of lead-time between blood collection and diagnosis. With lead times 6 months, ovarian cancer detection sensitivity at 0.98 specificity (SE98) varied from 0.19 [95% CI 0.08-0.40] for CTAG1A, CTAG2 and NUDT1 to 0.23 [0.10-0.44] for P53 (0.33 [0.11-0.68] for high-grade serous tumors). However, at longer lead-times, the ability of these AAb markers to distinguish future ovarian cancer cases from controls declined rapidly; at lead times >1 year, SE98 estimates were close to zero (all invasive cases, range: 0.01-0.11). Compared to CA125 alone, combined logistic regression scores of AAbs and CA125 did not improve detection sensitivity at equal level of specificity. The added value of these selected AAbs as markers for ovarian cancer beyond CA125 for early detection is therefore limited. What's new? Could autoantibodies against tumor antigens provide an early warning system for ovarian cancer? These authors tested how well certain antibodies detected ovarian cancer. They selected four candidate antibodies, to p53, CTAG1A, CTAG2 and NUDT11 proteins, which appear in elevated levels in cancer patients. None of them performed well as a herald of burgeoning cancer. They did not perform any better than the best currently available biomarker, CA125, and as lead times increased past 6 months prediagnosis, the effectiveness diminished. Surprisingly, elevated antibodies appeared in quite a few of the control samples, suggesting they might not be as cancer-specific as expected.
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| 17. |
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| 18. |
- Li, Xingru, 1987-
(författare)
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Wilms' tumor gene 1 in different types of cancer
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The Wilms’ tumor gene 1 (WT1) was first reported as a tumor suppressor gene in Wilms’ tumor. However, later studies have shown the oncogenic properties of WT1 in a variety of tumors. It was recently proposed that WT1 was a chameleon gene, due to its dual functions in tumorigenesis. We aimed to investigate the clinical significance of WT1 as biomarker in acute myeloid leukemia (AML) and clear cell renal cell carcinoma (ccRCC) and to elucidate the function of WT1 as an oncogene in squamous cell carcinoma of head and neck (SCCHN).In AML, it was suggested that WT1 expression was an applicable marker of minimal residual disease (MRD). In adult patients with AML, we found a good correlation between WT1 expression levels normalized to two control genes, β-actin and ABL. Outcome could be predicted by a reduction in WT1 expression in bone marrow (≥ 1-log) detected less than 1 month after diagnosis, when β-actin was used as control. Also, irrespective of the control gene used, outcome could be predicted by a reduction in WT1 expression in peripheral blood (≥ 2-log) detected between 1 and 6 months after treatment initiation.Previous studies in RCC demonstrated that WT1 acted as a tumor suppressor. Thus, we tested whether single nucleotide polymorphisms (SNPs) or mutations in WT1 might be associated with WT1 expression and clinical outcome in patients with ccRCC. We performed sequencing analysis on 10 exons of the WT1 gene in a total of 182 patient samples, and we identified six different SNPs in the WT1 gene. We found that at least one or two copies of the minor allele were present in 61% of ccRCC tumor samples. However, no correlation was observed between WT1 SNP genotypes and RNA expression levels. Moreover, none of the previously reported WT1 mutations were found in ccRCC. Nevertheless, we found that a favorable outcome was associated the homozygous minor allele for WT1 SNP. We then further investigated whether WT1 methylation was related to WT1 expression and its clinical significance. Methylation array and pyrosequencing analyses showed that the WT1 promoter region CpG site, cg22975913, was the most frequently hypermethylated CpG site. We found a trend that showed nearly significant correlation between WT1 mRNA levels and hypermethylation in the 5’-untranslated region. Hypermethylation in the WT1 CpG site, cg22975913, was found to be associated with patient age and a worse prognosis.One previous study reported that WT1 was overexpressed in SCCHN. That finding suggested that WT1 might play a role in oncogenesis. We found that both WT1 and p63 could promote cell proliferation. A positive correlation between WT1 and p63 expression was observed, and we identified p63 as a WT1 target gene. Furthermore, several known WT1 and p63 target genes were affected by knocking down WT1. Also, co-immunoprecipitation analyses demonstrated a protein interaction between WT1 and p53.In summary, WT1 gene expression can provide useful information for MRD detection during treatment of patients with AML. In RCC, our results suggested that the prognostic impact of WT1 SNPs was limited to the subgroup of patients that were homozygous for the minor allele, and that WT1 promoter hypermethylation could be used as a prognostic biomarker. In SCCHN, WT1 and p63 acted as oncogenes by affecting multiple genes involved in cancer cell growth.
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| 19. |
- Loderer, Christoph, et al.
(författare)
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Non-host class II ribonucleotide reductase in Thermus viruses : sequence adaptation and host interaction
- 2019
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Ingår i: PeerJ. - : PeerJ Incorporation. - 2167-8359. ; 7, s. 1-17
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Tidskriftsartikel (refereegranskat)abstract
- Ribonucleotide reductases (RNR) are essential enzymes for all known life forms. Their current taxonomic distribution suggests extensive horizontal gene transfer e.g., by processes involving viruses. To improve our understanding of the underlying processes, we characterized a monomeric class II RNR (NrdJm) enzyme from a Thermus virus, a subclass not present in any sequenced Thermus spp. genome. Phylogenetic analysis revealed a distant origin of the nrdJm gene with the most closely related sequences found in mesophiles or moderate thermophiles from the Firmicutes phylum. GC-content, codon usage and the ratio of coding to non-coding substitutions (dN/dS) suggest extensive adaptation of the gene in the virus in terms of nucleotide composition and amino acid sequence. The NrdJm enzyme is a monomeric B-12-dependent RNR with nucleoside triphosphate specificity. It exhibits a temperature optimum at 60-70 degrees C, which is in the range of the growth optimum of Thermus spp. Experiments in combination with the Thermus thermophilus thioredoxin system show that the enzyme is able to retrieve electrons from the host NADPH pool via host thioredoxin and thioredoxin reductases. This is different from other characterized viral RNRs such as T4 phage RNR, where a viral thioredoxin is present. We hence show that the monomeric class II RNR, present in Thermus viruses, was likely transferred from an organism phylogenetically distant from the one they were isolated from, and adapted to the new host in genetic signature and amino acids sequence.
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| 20. |
- Lundin, Andreas, et al.
(författare)
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Effect of Screening and Advising on Alcohol Habits in Sweden : A Repeated Population Survey Following Nationwide Implementation of Screening and Brief Intervention
- 2017
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Ingår i: Alcohol and Alcoholism. - : Oxford University Press (OUP). - 0735-0414 .- 1464-3502. ; 52:2, s. 190-196
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Tidskriftsartikel (refereegranskat)abstract
- AIMS: To examine: (a) to what extent individuals in contact with heath care had been asked and advised on their alcohol habits; (b) how self-reports of alcohol consumption and patient characteristics affected the probability of being asked and advised on alcohol consumption; (c) the potential effect of alcohol advice on readiness and ability to change, across levels of high alcohol consumption.METHODS: A repeated cross-sectional public health postal questionnaire in Uppsala County among 18-84 year old, covering a period of a national programme encouraging alcohol screening, brief interventions and motivational interviewing (2004-2012). Response rates were 65.5-52.2%. Respondent who stated that they had visited health-care services had a further question on whether the staff asked questions about habits including alcohol, and whether the staff had given them advice concerning the same habits. AUDIT-C was the measure of alcohol consumption, and there was a question on wanting to cut down on drinking and/or needing support to do so.RESULTS: Screening for and advising patients on alcohol consumption increased during the period, but there were no decreases in population-level consumption. Screening occurred independent of self-reports of AUDIT-C and varied with other individual characteristics. Advice was associated with AUDIT-C score. Being advised increased the likelihood of wanting to reduce drinking, both among those scoring above the national hazardous consumption levels and at higher scores.CONCLUSIONS: Screening and advising on alcohol habits in health care impacted individual readiness and ability to change. Population-level effects have yet to be proven.SHORT SUMMARY: Screening for and advising patients on alcohol consumption increased following a national programme encouraging alcohol screening, brief interventions and motivational interviewing. Overall consumption levels remained unchanged. Screening was largely systematic. The positive effect of advice on wanting to cut back drinking was similar in moderate and high drinkers.
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