| 1. |
- Groenen, M. A., et al.
(författare)
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Analyses of pig genomes provide insight into porcine demography and evolution
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 491:7424, s. 393-398
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Tidskriftsartikel (refereegranskat)abstract
- For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars approximately 1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
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| 2. |
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| 3. |
- Holmberg, M., et al.
(författare)
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Treatment outcome 6-10 years after diagnosis of hyperthyroidism in 2916 patients : a longitudinal evaluation of a swedish incidence cohort
- 2018
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Ingår i: Thyroid. - : Mary Ann Liebert. - 1050-7256 .- 1557-9077. ; :S1
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Treatment of Graves’ disease (GD) and toxic nodular goiter (TNG) has the objectives to cure hyperthyroidism, prevent recurrent disease and preserve thyroid function. Treatment efficacies and long-termout comes of antithyroid drugs (ATD), radioactive iodine (RAI) or surgery varies in the literature. We report outcome of treatment, cure rate and risk factors for relapse for GD and TNG in an unselected cohort. A prospective incidence-cohort of de novo diagnosed GD and TNG patients (n = 2916) from 2003-05, were invited to a follow-up 6 - 10 years after diagnosis. Questionnaires were sent to 2430 patients regarding treatments, cure rate, recurrence, quality of life, demographic data, comorbidities and life-style factors. Patients were treated according to clinical routine with ATD, RAI or surgery. Of those included, 1186 (83.3%) had GD and 237 (16.7%) had TNG. In GD patients, 351 (45.3%), 264 (81.5%), and 52 (96.3%) were cured by ATD, RAI or surgery respectively as first line treatment. Of those, 77.0%, 15.4% and 3.8% respectively were without levothyr-oxine supplementation at follow-up at 8 – 0.9 years. Including all treatment modalities, 851 (71.8%) of GD patients were cured within one treatment period. At follow-up, 278 (23%) of GD patients had been operated. In TNG patients, RAI cured 88.6% and surgery 92.9%, whereof 52/154 (33.8%) and 3/15 (20%) had no levothyroxine supplementation post RAI and surgery, respectively.The proportion that did not feel fully recovered at follow-up was 25.3% of GD and 18.1% of the TNG patients. Overall, treatment of hyperthyroidism results in preserved thyroid function only in 35.3% and 44.7% of GD and TNG cases, respectively. As many as 23.4% of the GD patients end up with surgery although only 4.6% choose it from the beginning. Our treatment tradition cures 71.8% of GD patients and 78.1% of TNG patients within one treatment period. The high number of patients who do not feel recovered 6 -10 years after hyperthyroidism in GD and TNG is are minder of the chronic nature of hyperthyroidism.
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| 4. |
- Berglund, Åsa M. M., 1978-, et al.
(författare)
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Effects on the food-web structure and bioaccumulation patterns of organic contaminants in a climate-altered Bothnian Sea mesocosms
- 2023
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Ingår i: Frontiers in Marine Science. - : Frontiers Media S.A.. - 2296-7745. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Climate change is expected to alter global temperature and precipitation patterns resulting in complex environmental impacts. The proposed higher precipitation in northern Scandinavia would increase runoff from land, hence increase the inflow of terrestrial dissolved organic matter (tDOM) in coastal regions. This could promote heterotrophic bacterial production and shift the food web structure, by favoring the microbial food web. The altered climate is also expected to affect transport and availability of organic micropollutants (MPs), with downstream effects on exposure and accumulation in biota. This study aimed to assess climate-induced changes in a Bothnian Sea food web structure as well as bioaccumulation patterns of MPs. We performed a mesocosms-study, focusing on aquatic food webs with fish as top predator. Alongside increased temperature, mesocosm treatments included tDOM and MP addition. The tDOM addition affected nutrient availability and boosted both phytoplankton and heterotrophic bacteria in our fairly shallow mesocosms. The increased tDOM further benefitted flagellates, ciliates and mesozooplankton, while the temperature increase and MP addition had minor effect on those organism groups. Temperature, on the other hand, had a negative impact on fish growth and survival, whereas tDOM and MP addition only had minor impact on fish. Moreover, there were indications that bioaccumulation of MPs in fish either increased with tDOM addition or decreased at higher temperatures. If there was an impact on bioaccumulation, moderately lipophilic MPs (log Kow 3.6 - 4.6) were generally affected by tDOM addition and more lipophilic MPs (log Kow 3.8 to 6.4) were generally affected by increased temperature. This study suggest that both increased temperatures and addition of tDOM likely will affect bioaccumulation patterns of MPs in shallow coastal regions, albeit with counteracting effects.
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| 5. |
- Byström, Sanna, et al.
(författare)
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Affinity Proteomic Profiling of Plasma, Cerebrospinal Fluid, and Brain Tissue within Multiple Sclerosis
- 2014
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 13:11, s. 4607-4619
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Tidskriftsartikel (refereegranskat)abstract
- The brain is a vital organ and because it is well shielded from the outside environment, possibilities for noninvasive analysis are often limited. Instead, fluids taken from the spinal cord or circulatory system are preferred sources for the discovery of candidate markers within neurological diseases. In the context of multiple sclerosis (MS), we applied an affinity proteomic strategy and screened 22 plasma samples with 4595 antibodies (3450 genes) on bead arrays, then defined 375 antibodies (334 genes) for targeted analysis in a set of 172 samples and finally used 101 antibodies (43 genes) on 443 plasma as well as 573 cerebrospinal spinal fluid (CSF) samples. This revealed alteration of protein profiles in relation to MS subtypes for IRF8, IL7, METTL14, SLC30A7, and GAP43. Respective antibodies were subsequently used for immunofluorescence on human post-mortem brain tissue with MS pathology for expression and association analysis. There, antibodies for IRF8, IL7, and METTL14 stained neurons in proximity of lesions, which highlighted these candidate protein targets for further studies within MS and brain tissue. The affinity proteomic translation of profiles discovered by profiling human body fluids and tissue provides a powerful strategy to suggest additional candidates to studies of neurological disorders.
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| 6. |
- Ekman-Ordeberg, G, et al.
(författare)
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Low molecular weight heparin stimulates myometrial contractility and cervical remodeling in vitro
- 2009
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Ingår i: Acta Obstet Gynecol Scand. - : Wiley. ; 88:9, s. 984-989
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: The low molecular weight heparin, Dalteparin, shortens human labor time. The aim of this study was to investigate if the mechanism behind this effect involves myometrial contractility and cervical ripening and if the anticoagulative activity is necessary for its effect. DESIGN: Experimental in vitro study. SETTING: Lund University and Karolinska Institute, Sweden. METHODS: The effect of low molecular weight heparins with or without anticoagulative properties on myometrial contractility was measured in vitro on smooth muscle strips from biopsies obtained at elective cesarean sections. The effects on cervical ripening were assessed in cervical fibroblasts cultured from explants of cervical biopsies obtained at delivery. MAIN OUTCOME MEASURES: Mean force and number of contractions in uterine smooth muscle strips and interleukin-8 (IL-8) secretion in cervical fibroblasts. RESULTS: Myometrial smooth muscle strips pretreated with low molecular weight heparins showed increased contractile activity compared to untreated smooth muscle strips. Secretion of IL-8 from cultured cervical fibroblasts was significantly increased after treatment with low molecular weight heparin. Both these effects were independent of anticoagulative activity of the low molecular weight heparin. CONCLUSIONS: A possible underlying mechanism for the shortened labor time after low molecular weight heparin treatment is enhanced myometrial contractility and an increased IL-8 secretion in cervical fibroblast, mimicking the final cervical ripening in vivo. Our data support the notion that anticoagulant activity is not required to promote labor.
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| 7. |
- Fredolini, Claudia, et al.
(författare)
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Systematic assessment of antibody selectivity in plasma based on a resource of enrichment profiles
- 2019
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- There is a strong need for procedures that enable context and application dependent validation of antibodies. Here, we applied a magnetic bead assisted workflow and immunoprecipitation mass spectrometry (IP-MS/MS) to assess antibody selectivity for the detection of proteins in human plasma. A resource was built on 414 IP experiments using 157 antibodies (targeting 120 unique proteins) in assays with heat-treated or untreated EDTA plasma. For each protein we determined their antibody related degrees of enrichment using z-scores and their frequencies of identification across all IP assays. Out of 1,313 unique endogenous proteins, 426 proteins (33%) were detected in >20% of IPs, and these background components were mainly comprised of proteins from the complement system. For 45% (70/157) of the tested antibodies, the expected target proteins were enriched (z-score >= 3). Among these 70 antibodies, 59 (84%) co-enriched other proteins beside the intended target and mainly due to sequence homology or protein abundance. We also detected protein interactions in plasma, and for IGFBP2 confirmed these using several antibodies and sandwich immunoassays. The protein enrichment data with plasma provide a very useful and yet lacking resource for the assessment of antibody selectivity. Our insights will contribute to a more informed use of affinity reagents for plasma proteomics assays.
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| 8. |
- Häggmark, Anna, et al.
(författare)
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Antibody-based profiling of cerebrospinal fluid within multiple sclerosis
- 2013
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Ingår i: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 13:15, s. 2256-2267
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Tidskriftsartikel (refereegranskat)abstract
- Antibody suspension bead arrays have proven to enable multiplexed and high-throughput protein profiling in unfractionated plasma and serum samples through a direct labeling approach. We here describe the development and application of an assay for protein profiling of cerebrospinal fluid (CSF). While setting up the assay, systematic intensity differences between sample groups were observed that reflected inherent sample specific total protein amounts. Supplementing the labeling reaction with BSA and IgG diminished these differences without impairing the apparent sensitivity of the assay. We also assessed the effects of heat treatment on the analysis of CSF proteins and applied the assay to profile 43 selected proteins by 101 antibodies in 339 CSF samples from a multiple sclerosis (MS) cohort. Two proteins, GAP43 and SERPINA3 were found to have a discriminating potential with altered intensity levels between sample groups. GAP43 was detected at significantly lower levels in secondary progressive MS compared to early stages of MS and the control group of other neurological diseases. SERPINA3 instead was detected at higher levels in all MS patients compared to controls. The developed assay procedure now offers new possibilities for broad-scale protein profiling of CSF within neurological disorders.
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| 9. |
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| 10. |
- Sj?lin, G., et al.
(författare)
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The Long-Term Outcome of Treatment for Graves' Hyperthyroidism
- 2019
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Ingår i: Thyroid. - : Mary Ann Liebert Inc. - 1050-7256 .- 1557-9077. ; 29:11, s. 1545-1557
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Tidskriftsartikel (refereegranskat)abstract
- Background: The treatment efficacy of antithyroid drug (ATD) therapy, radioactive iodine (I-131), or surgery for Graves' hyperthyroidism is well described. However, there are a few reports on the long-term total outcome of each treatment modality regarding how many require levothyroxine supplementation, the need of thyroid ablation, or the individual patient's estimation of their recovery. Methods: We conducted a pragmatic trial to determine the effectiveness and adverse outcome in a patient cohort newly diagnosed with Graves' hyperthyroidism between 2003 and 2005 (n = 2430). The patients were invited to participate in a longitudinal study spanning 8 +/- 0.9 years (mean +/- standard deviation) after diagnosis. We were able to follow 1186 (60%) patients who had been treated with ATD, I-131, or surgery. We determined the mode of treatment, remission rate, recurrence, quality of life, demographic data, comorbidities, and lifestyle factors through questionnaires and a review of the individual's medical history records. Results: At follow-up, the remission rate after first-line treatment choice with ATD was 45.3% (351/774), with I-131 therapy 81.5% (324/264), and with surgery 96.3% (52/54). Among those patients who had a second course of ATD, 29.4% achieved remission (vs. the 45.3% after the first course of ATD). The total number of patients who had undergone ablative treatment was 64.3% (763/1186), of whom 23% (278/1186) had received surgery, 43% (505/1186) had received I-131 therapy, including 2% (20/1186) who had received both surgery and I-131. Patients who received ATD as first-line treatment and possibly additional ATD had 49.7% risk (385/774) of having undergone ablative treatment at follow-up. Levothyroxine replacement was needed in 23% (81/351) of the initially ATD treated in remission, in 77.3% (204/264) of the I-131 treated, and in 96.2% (50/52) of the surgically treated patients. Taken together after 6-10 years, and all treatment considered, normal thyroid hormone status without thyroxine supplementation was only achieved in 35.7% (423/1186) of all patients and in only 40.3% of those initially treated with ATD. The proportion of patients that did not feel fully recovered at follow-up was 25.3%. Conclusion: A patient selecting ATD therapy as the initial approach in the treatment of Graves' hyperthyroidism should be informed that they have only a 50.3% chance of ultimately avoiding ablative treatment and only a 40% chance of eventually being euthyroid without thyroid medication. Surprisingly, 1 in 4 patients did not feel fully recovered after 6-10 years. The treatment for Graves' hyperthyroidism, thus, has unexpected long-term consequences for many patients.
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| 11. |
- Åström, S U, et al.
(författare)
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Genetic interactions between a null allele of the RIT1 gene encoding an initiator tRNA-specific modification enzyme and genes encoding translation factors in Saccharomyces cerevisiae
- 1999
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Ingår i: Molecular General Genetics. - : Springer. - 0026-8925 .- 1432-1874. ; 261:6, s. 967-976
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Tidskriftsartikel (refereegranskat)abstract
- The Saccharomyces cerevisiae gene RIT1 encodes a phospho-ribosyl transferase that exclusively modifies the initiator tRNA (tRNAMet(i)) by the addition of a 2'-O-ribosyl phosphate group to Adenosine 64. As a result, tRNAMet(i) is prevented from participating in the elongation steps of protein synthesis. We previously showed that the modification is not essential for the function of tRNAMet(i) in the initiation of translation, since rit1 null strains are viable and show no obvious growth defects. Here, we demonstrate that yeast strains in which a rit1 null allele is combined with mutations in any of the genes for the three subunits of eukaryotic initiation factor-2 (eIF-2), or with disruption alleles of two of the four initiator methionine tRNA (IMT) genes, show synergistic growth defects. A multicopy plasmid carrying an IMT gene can alleviate these defects. On the other hand, introduction of a high-copy-number plasmid carrying the TEF2 gene, which encodes the eukaryotic elongation factor 1alpha (eEF-1alpha), into rit1 null strains with two intact IMT genes had the opposite effect, indicating that increased levels of eEF-1alpha are deleterious to these strains, presumably due to sequestration of the unmodified met-tRNAMet(i) for elongation. Thus, under conditions in which the components of the ternary met-tRNAMet(i):GTP:eIF-2 complex become limiting or are functionally impaired, the presence of the 2'-O-ribosyl phosphate modification in tRNAMet(i) is important for the provision of adequate amounts of tRNAMet(i) for formation of this ternary complex.
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| 12. |
- Andersson, Jens, et al.
(författare)
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Plastic reources polymorphism : effects or resource availability on Arctic char (Salvelinus alpinus) morphology
- 2005
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Ingår i: Biological Journal of the Linnean Society. - London : Acad. P.. - 0024-4066 .- 1095-8312. ; 85:3, s. 341-351
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Tidskriftsartikel (refereegranskat)abstract
- Resource polymorphism has been suggested to be a platform for speciation. In some cases resource polymorphism depends on phenotypic plasticity but in other cases on genetic differences between morphotypes, which in turn has been suggested to be the ongoing development of a species pair. Here we study environmentally induced morphological differences in two age classes of Arctic char (Salvelinus alpinus) influencing char performance and diet in relation to resource availability. We found that structurally complex habitats with relatively lower zooplankton densities gave rise to individuals with a deeper body, and a downward positioned tip of the snout compared with individuals from structurally simple habitats with relatively higher zooplankton densities for both age classes. Environment also had an effect on foraging efficiency on zooplankton, with fish from structurally simple habitats had a higher foraging rate than fish from structurally complex habitats. Diet analyses showed that resource use in char mainly depends on the relative abundance of different resources. Therefore, to gain further understanding of resource polymorphism we suggest that future studies must include population dynamic feedbacks by the resources on the consumers.
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| 13. |
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| 14. |
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| 15. |
- Björk, Glenn R, et al.
(författare)
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Prevention of translational frameshifting by the modified nucleoside 1-methylguanosine
- 1989
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Ingår i: Science. - 0036-8075 .- 1095-9203. ; 244:4907, s. 986-989
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Tidskriftsartikel (refereegranskat)abstract
- The methylated nucleoside 1-methylguanosine (m1G) is present next to the 3' end of the anticodon (position 37) in all transfer RNAs (tRNAs) that read codons starting with C except in those tRNAs that read CAN codons. All of the three proline tRNA species, which read CCN codons in Salmonella typhimurium, have been sequenced and shown to contain m1G in position 37. A mutant of S. typhimurium that lacks m1G in its tRNA when grown at temperatures above 37 degrees C, has now been isolated. The mutation (trmD3) responsible for this methylation deficiency is in the structural gene (trmD) for the tRNA(m1G37)methyltransferase. Therefore, the three proline tRNAs in the trmD3 mutant have an unmodified guanosine at position 37. Furthermore, the trmD3 mutation also causes at least one of the tRNAPro species to frequently shift frame when C's are present successively in the message. Thus, m1G appears to prevent frameshifting. The data from eubacteria apply to both eukaryotes and archaebacteria.
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| 16. |
- Braendengen, Morten, et al.
(författare)
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Randomized phase III study comparing preoperative radiotherapy with chemoradiotherapy in nonresectable rectal cancer
- 2008
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Ingår i: Journal of Clinical Oncology. - 0732-183X .- 1527-7755. ; 26:22, s. 3687-3694
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Tidskriftsartikel (refereegranskat)abstract
- PURPOSE: Preoperative chemoradiotherapy is considered standard treatment for locally advanced rectal cancer, although the scientific evidence for the chemotherapy addition is limited. This trial investigated whether chemotherapy as part of a multidisciplinary treatment approach would improve downstaging, survival, and relapse rate. PATIENTS AND METHODS: The randomized study included 207 patients with locally nonresectable T4 primary rectal carcinoma or local recurrence from rectal carcinoma in the period 1996 to 2003. The patients received either chemotherapy (fluorouracil/leucovorin) administered concurrently with radiotherapy (50 Gy) and adjuvant for 16 weeks after surgery (CRT group, n = 98) or radiotherapy alone (50 Gy; RT group, n = 109). RESULTS: The two groups were well balanced according to pretreatment characteristics. An R0 resection was performed in 82 patients (84%) in the CRT group and in 74 patients (68%) in the RT group (P = .009). Pathologic complete response was seen in 16% and 7%, respectively. After an R0 + R1 resection, local recurrence was found in 5% and 7%, and distant metastases in 26% and 39%, respectively. Local control (82% v 67% at 5 years; log-rank P = .03), time to treatment failure (63% v 44%; P = .003), cancer-specific survival (72% v 55%; P = .02), and overall survival (66% v 53%; P = .09) all favored the CRT group. Grade 3 or 4 toxicity, mainly GI, was seen in 28 (29%) of 98 and six (6%) of 109, respectively (P = .001). There was no difference in late toxicity. CONCLUSION: CRT improved local control, time to treatment failure, and cancer-specific survival compared with RT alone in patients with nonresectable rectal cancer. The treatments were well tolerated.
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| 17. |
- Byström, Jonas, et al.
(författare)
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Inducible CYP2J2 and its product 11,12-EET promotes bacterial phagocytosis : a role for CYP2J2 deficiency in the pathogenesis of Crohn's disease?
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 8:9
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Tidskriftsartikel (refereegranskat)abstract
- The epoxygenase CYP2J2 has an emerging role in inflammation and vascular biology. The role of CYP2J2 in phagocytosis is not known and its regulation in human inflammatory diseases is poorly understood. Here we investigated the role of CYP2J2 in bacterial phagocytosis and its expression in monocytes from healthy controls and Crohns disease patients. CYP2J2 is anti-inflammatory in human peripheral blood monocytes. Bacterial LPS induced CYP2J2 mRNA and protein. The CYP2J2 arachidonic acid products 11,12-EET and 14,15-EET inhibited LPS induced TNFα release. THP-1 monocytes were transformed into macrophages by 48h incubation with phorbol 12-myristate 13-acetate. Epoxygenase inhibition using a non-selective inhibitor SKF525A or a selective CYP2J2 inhibitor Compound 4, inhibited E. coli particle phagocytosis, which could be specifically reversed by 11,12-EET. Moreover, epoxygenase inhibition reduced the expression of phagocytosis receptors CD11b and CD68. CD11b also mediates L. monocytogenes phagocytosis. Similar, to E. coli bioparticle phagocytosis, epoxygenase inhibition also reduced intracellular levels of L. monocytogenes, which could be reversed by co-incubation with 11,12-EET. Disrupted bacterial clearance is a hallmark of Crohn's disease. Unlike macrophages from control donors, macrophages from Crohn's disease patients showed no induction of CYP2J2 in response to E. coli. These results demonstrate that CYP2J2 mediates bacterial phagocytosis in macrophages, and implicates a defect in the CYP2J2 pathway may regulate bacterial clearance in Crohn's disease.
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| 18. |
- Byström, JW, et al.
(författare)
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Serological assessment of SARS-CoV-2 exposure in northern Sweden by the use of at-home sampling to meet geographical challenges in rural regions
- 2022
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Ingår i: medRxiv : the preprint server for health sciences. - : Cold Spring Harbor Laboratory.
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The current SARS-CoV-2 pandemic has highlighted a need for easy and safe blood sampling in combination with accurate serological methodology. Venipuncture is usually performed by trained staff at health care centers. Long travel distances may introduce a bias of testing towards relatively large communities with close access to health care centers. Rural regions may thus be overlooked. Here, we demonstrate a sensitive method to measure antibodies to the S-protein of SARS-CoV-2. We adapted and optimized this assay for clinical use together with capillary blood sampling to meet the geographical challenges of serosurveillance. Finally, we tested remote at-home capillary blood sampling together with centralized assessment of S-specific IgG in a rural region of northern Scandinavia that encompasses 55,185 sq kilometers. We conclude that serological assessment from capillary blood sampling gives comparable results as analysis of venous blood. Importantly, at-home sampling enabled citizens living in remote rural areas access to centralized and sensitive laboratory antibody tests.
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| 19. |
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| 20. |
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| 21. |
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| 22. |
- Byström, Roberth, et al.
(författare)
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SOD1 mutations targeting surface hydrogen bonds promote ALS without reducing apo-state stability
- 2010
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Ingår i: Journal of Biological Chemistry. - : The American Society for Biochemistry and Molecular Biology. - 0021-9258 .- 1083-351X. ; 285:25, s. 19544-52
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Tidskriftsartikel (refereegranskat)abstract
- In good accord with the protein-aggregation hypothesis for neurodegenerative diseases, ALS-associated SOD1 mutations are found to reduce structural stability or net repulsive charge. Moreover there are weak indications that the ALS disease progression rate is correlated with the degree of mutational impact on the apo-SOD1 structure. A bottleneck for obtaining more conclusive information about these structure-disease relationships, however, is the large intrinsic variability in patient survival times and insufficient disease statistics for the majority of ALS-provoking mutations. As an alternative test of the structure-disease relationship we focus here on the SOD1 mutations that appear to be outliers in the data set. The results identify several ALS-provoking mutations whose only effect on apo SOD1 is the elimination or introduction of a single charge, i.e., D76V/Y, D101N and N139D/K. The thermodynamic stability and folding behaviour of these mutants are indistinguishable from the wildtype control. Moreover, D101N is an outlier in the plot of stability loss vs. patient survival time by having rapid disease progression. Common to the identified mutations is that they truncate conserved salt-links and/or H-bond networks in the functional loops IV or VII. The results show that the local impact of ALS-associated mutations on the SOD1 molecule can sometimes overrun their global effects on apo-state stability and net repulsive charge, and point at the analysis of property outliers as an efficient strategy for mapping out new ALS-provoking features.
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| 23. |
- Byström, Roberth, et al.
(författare)
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SOD1 Mutations Targeting Surface Hydrogen Bonds Promote Amyotrophic Lateral Sclerosis without Reducing Apo-state Stability
- 2010
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Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 285:25, s. 19544-19552
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Tidskriftsartikel (refereegranskat)abstract
- In good accord with the protein aggregation hypothesis for neurodegenerative diseases, ALS-associated SOD1 mutations are found to reduce structural stability or net repulsive charge. Moreover there are weak indications that the ALS disease progression rate is correlated with the degree of mutational impact on the apoSOD1 structure. A bottleneck for obtaining more conclusive information about these structure-disease relationships, however, is the large intrinsic variability in patient survival times and insufficient disease statistics for the majority of ALS- provoking mutations. As an alternative test of the structure- disease relationship we focus here on the SOD1 mutations that appear to be outliers in the data set. The results identify several ALS- provoking mutations whose only effect on apoSOD1 is the elimination or introduction of a single charge, i.e. D76V/Y, D101N, and N139D/K. The thermodynamic stability and folding behavior of these mutants are indistinguishable from the wild-type control. Moreover, D101N is an outlier in the plot of stability loss versus patient survival time by having rapid disease progression. Commonto the identified mutations is that they truncate conserved salt-links and/or H-bond networks in the functional loops IV or VII. The results show that the local impact of ALS- associated mutations on the SOD1 molecule can sometimes overrun their global effects on apo-state stability and net repulsive charge, and point at the analysis of property outliers as an efficient strategy for mapping out new ALS- provoking features.
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| 24. |
- Byström, Sanna
(författare)
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Affinity assays for profiling disease-associated proteins in human plasma
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Affinity-based proteomics offers opportunities for the discovery and validation of disease-associated proteins in human body fluids. This thesis describes the use of antibody-based immunoassays for multiplexed analysis of proteins in human plasma, serum and cerebrospinal fluid (CSF). This high-throughput method was applied with the objective to identify proteins associated to clinical variables. The main work in this thesis was conducted within the diseases of multiple sclerosis and malignant melanoma, as well as mammographic density, a risk factor for breast cancer.The suspension bead array (SBA) technology has been the main method for the work presented in this thesis (Paper I-IV). SBA assays and other affinity proteomic technologies were introduced for protein profiling of sample material obtained from clinical collaborators and biobanks. Perspectives on the validation of antibody selectivity by means of e.g. immuno-capture mass spectrometry are also provided.Paper I describes the development and application of a protocol for multiplexed pro- tein profiling of CSF. The analysis of 340 CSF samples from patients with multiple sclerosis and other neurological disease revealed proteins with potential association to disease progression (GAP43) and inflammation (SERPINA3). Paper II continued on this work with an extended investigation of more than 1,000 clinical samples and included both plasma and CSF collected from the same patients. Comparison of disease subtypes and controls revealed five plasma proteins of potential diagnostic relevance, such as IRF8 and GAP43. The previously reported associations for GAP43 and SERPINA3 in CSF was confirmed. Subsequent immunohistochemical analysis of post-mortem brain tissue revealed differential protein expression in disease affected areas. In Paper III, 150 serum samples from patients with cutaneous malignant melanoma were analyzed. Protein profiles from antibody bead arrays suggested three proteins (RGN, MTHFD1L, STX7) of differential abundance between patients with no disease recurrence and low tumor thickness (T-stage 1 and 2) compared to patients with high tumor thickness (T-stage 3 and 4) and disease recurrence. We observed MTHFD1L expression in tissue of a majority of patients, while expression of STX7 in melanoma tissue had been reported previously. Paper IV describes the analysis of protein in plasma in relation to mammographic breast density (MD), one of the strongest risk factors for the development of breast cancers. More than 1,300 women without prior history of breast cancer were screened. Linear associations to MD in two independent sample sets were found for 11 proteins, which are expressed in the breast and involved in tissue homeostasis, DNA repair, cancer development and/or progression in MD.In conclusion, this thesis describes the use of multiplexed antibody bead arrays for protein profiling of serum, plasma and CSF, and it shortlists disease associated proteins for further validation studies.
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| 25. |
- Byström, Sanna, et al.
(författare)
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Affinity proteomic profiling of plasma for proteins associated to area-based mammographic breast density
- 2018
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Ingår i: Breast Cancer Research. - : BIOMED CENTRAL LTD. - 1465-5411 .- 1465-542X. ; 20
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Tidskriftsartikel (refereegranskat)abstract
- Background: Mammographic breast density is one of the strongest risk factors for breast cancer, but molecular understanding of how breast density relates to cancer risk is less complete. Studies of proteins in blood plasma, possibly associated with mammographic density, are well-suited as these allow large-scale analyses and might shed light on the association between breast cancer and breast density. Methods: Plasma samples from 1329 women in the Swedish KARMA project, without prior history of breast cancer, were profiled with antibody suspension bead array (SBA) assays. Two sample sets comprising 729 and 600 women were screened by two different SBAs targeting a total number of 357 proteins. Protein targets were selected through searching the literature, for either being related to breast cancer or for being linked to the extracellular matrix. Association between proteins and absolute area-based breast density (AD) was assessed by quantile regression, adjusting for age and body mass index (BMI). Results: Plasma profiling revealed linear association between 20 proteins and AD, concordant in the two sets of samples (p < 0.05). Plasma levels of seven proteins were positively associated and 13 proteins negatively associated with AD. For eleven of these proteins evidence for gene expression in breast tissue existed. Among these, ABCC11, TNFRSF10D, F11R and ERRF were positively associated with AD, and SHC1, CFLAR, ACOX2, ITGB6, RASSF1, FANCD2 and IRX5 were negatively associated with AD. Conclusions: Screening proteins in plasma indicates associations between breast density and processes of tissue homeostasis, DNA repair, cancer development and/or progression in breast cancer. Further validation and follow-up studies of the shortlisted protein candidates in independent cohorts will be needed to infer their role in breast density and its progression in premenopausal and postmenopausal women.
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| 26. |
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| 27. |
- Byström, Sanna, et al.
(författare)
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Affinity Proteomics Exploration of Melanoma Identifies Proteins in Serum with Associations to T-Stage and Recurrence
- 2017
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Ingår i: Translational Oncology. - : Neoplasia Press, Inc.. - 1944-7124 .- 1936-5233. ; 10:3, s. 385-395
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Blood-based proteomic profiling may aid and expand our understanding of diseases and their different phenotypes. The aim of the presented study was to profile serum samples from patients with malignant melanoma using affinity proteomic assays to describe proteins in the blood stream that are associated to stage or recurrence of melanoma. MATERIAL AND METHODS: Multiplexed protein analysis was conducted using antibody suspension bead arrays. A total of 232 antibodies against 132 proteins were selected from (i) a screening with 4595 antibodies and 32 serum samples from melanoma patients and controls, (ii) antibodies used for immunohistochemistry, (iii) protein targets previously related with melanoma. The analysis was performed with 149 serum samples from patients with malignant melanoma. Antibody selectivity was then assessed by Western blot, immunocapture mass spectrometry, and epitope mapping. Lastly, indicative antibodies were applied for IHC analysis of melanoma tissues. RESULTS: Serum levels of regucalcin (RGN) and syntaxin 7 (STX7) were found to be lower in patients with both recurring tumors and a high Breslow's thickness (T-stage 3/4) compared to low thickness (T-stage 1/2) without disease recurrence. Serum levels of methylenetetrahydrofolate dehydrogenase 1-like (MTHFD1L) were instead elevated in sera of T3/4 patients with recurrence. The analysis of tissue sections with S100A6 and MTHFD1L showed positive staining in a majority of patients with melanoma, and S100A6 was significantly associated to T-stage. CONCLUSIONS: Our findings provide a starting point to further study RGN, STX7, MTHFD1L and S100A6 in serum to elucidate their involvement in melanoma progression and to assess a possible contribution to support clinical indications.
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| 28. |
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| 29. |
- Courtois, Julien, et al.
(författare)
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A study of surface modification and anchoring techniques used in the preparation of monolithic microcolumns in fused silica capillaries.
- 2006
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Ingår i: Journal of Separation Science. - : Wiley. - 1615-9306 .- 1615-9314. ; 29:1, s. 14-24
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Tidskriftsartikel (refereegranskat)abstract
- Based on a survey of the literature on pretreatment of fused silica capillaries, 3 etching procedures and 11 silanization protocols based on the vinylic silane 3-((trimethoxysilyl)propyl) methacrylate (gamma-MAPS) were found to be most representative as a means of ensuring attachment of in situ prepared vinylic polymers. These techniques were applied to fused silica capillaries and the success in establishing the intended surface modification was assessed. X-ray photoelectron spectroscopy (XPS) was used to characterize the chemical state of the surface, providing information regarding presence of the reagent bound to the capillary. Wetting angles were measured and correlated with the XPS results. An adherence test was done by photopolymerization of a 2 mm long plug of 1,6-butanediol dimethacrylate in the prepared capillaries and evaluation of its ability to withstand applied hydraulic pressure. SEM was also performed in cases where the plug was released or other irregularities were observed. Finally, the roughness of the etched surface, considered to be of importance, was assessed by atomic force microscopy. Alkaline etching at elevated temperature provided a surface roughness promoting adhesion. The commonly used silanization protocols involving water in the silanization or washing steps gave inadequate surface treatment. The best silanization procedure was based on toluene as a solvent.
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| 30. |
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| 31. |
- Fredolini, Claudia, et al.
(författare)
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Immunocapture strategies in translational proteomics
- 2016
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Ingår i: Expert Review of Proteomics. - : Taylor & Francis. - 1478-9450 .- 1744-8387. ; 13:1, s. 83-98
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Forskningsöversikt (refereegranskat)abstract
- Aiming at clinical studies of human diseases, antibody-assisted assays have been applied to biomarker discovery and toward a streamlined translation from patient profiling to assays supporting personalized treatments. In recent years, integrated strategies to couple and combine antibodies with mass spectrometry-based proteomic efforts have emerged, allowing for novel possibilities in basic and clinical research. Described in this review are some of the field's current and emerging immunocapture approaches from an affinity proteomics perspective. Discussed are some of their advantages, pitfalls and opportunities for the next phase in clinical and translational proteomics.
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| 32. |
- Friant, S, et al.
(författare)
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Interactions between Ty1 retrotransposon RNA and the T and D regions of the tRNA(iMet) primer are required for initiation of reverse transcription in vivo
- 1998
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Ingår i: Molecular and Cellular Biology. - 0270-7306 .- 1098-5549. ; 18:2, s. 799-806
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Tidskriftsartikel (refereegranskat)abstract
- Reverse transcription of the Saccharomyces cerevisiae Ty1 retrotransposon is primed by tRNA(iMet) base paired to the primer binding site (PBS) near the 5' end of Ty1 genomic RNA. The 10-nucleotide PBS is complementary to the last 10 nucleotides of the acceptor stem of tRNA(iMet). A structural probing study of the interactions between the Ty1 RNA template and the tRNA(iMet) primer showed that besides interactions between the PBS and the 3' end of tRNA(iMet), three short regions of Ty1 RNA, named boxes 0, 1, and 2.1, interact with the T and D stems and loops of tRNA(iMet). To determine if these sequences are important for the reverse transcription pathway of the Ty1 retrotransposon, mutant Ty1 elements and tRNA(iMet) were tested for the ability to support transposition. We show that the Ty1 boxes and the complementary sequences in the T and D stems and loops of tRNA(iMet) contain bases that are critical for Ty1 retrotransposition. Disruption of 1 or 2 bp between tRNA(iMet) and box 0, 1, or 2.1 dramatically decreases the level of transposition. Compensatory mutations which restore base pairing between the primer and the template restore transposition. Analysis of the reverse transcription intermediates generated inside Ty1 virus-like particles indicates that initiation of minus-strand strong-stop DNA synthesis is affected by mutations disrupting complementarity between Ty1 RNA and primer tRNA(iMet).
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| 33. |
- Garskaite, Edita, et al.
(författare)
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Studying the application of fish-farming net-cleaning waste as fire-retardant for Scots pine (Pinus sylvestris L.) sapwood
- 2022
-
Ingår i: EFB Bioeconomy Journal. - : Elsevier. - 2667-0410. ; 2
-
Tidskriftsartikel (refereegranskat)abstract
- Optimising the exploitation of available waste resources for the recovery of their intrinsic value will be vital in the future circular economy society. Recovery of energy, nutrients and metals from waste streams is in focus today. This study aimed to evaluate the use of an aquaculture waste, i.e. the dried-solid waste discharge that generates by cleaning the fishing-nets, as a potential fire-retardancy promoter for Scots pine sapwood. As-received dried-solid waste from salmon-farming was calcined at different temperatures to evaluate material phase transformation and achieve homogeneous phase distribution. Thermal degradation of waste powders was studied by TG-FTIR gas analysis when annealing the material to temperatures up to 800°C, and the crystallinity, phase composition, morphology, elemental composition and particle sizes of as-received and calcined-waste materials at different temperatures were evaluated by XRD, FTIR, SEM/EDS, and TEM analyses. The flammability studies using cone calorimeter of Scots pine sapwood blocks treated with as-received and processed material is also reported and discussed. Results were promising, indicating that the aquaculture waste could be employed as an effective fire-retardant. The possibility of value-creation from waste discharges is enforced in this study so to promote the way towards waste valorisation and circular economy.
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| 34. |
- Glimelius, Bengt, et al.
(författare)
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A window of opportunity phase II study of enzastaurin in chemonaive patients with asymptomatic metastatic colorectal cancer
- 2010
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Ingår i: Annals of Oncology. - : Elsevier BV. - 0923-7534 .- 1569-8041. ; 21:5, s. 1020-1026
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Preclinically, protein kinase C and AKT activation can be inhibited by enzastaurin and reduce tumor growth of colorectal cancer cells. In asymptomatic patients with metastatic colorectal cancer (mCRC), enzastaurin activity was evaluated by measuring the 6-month progression-free survival (PFS) rate in a window study design. PATIENTS AND METHODS: Chemonaive patients with asymptomatic mCRC who did not require immediate chemotherapy-induced tumor reduction received a 400-mg thrice daily loading dose of enzastaurin on day 1 of cycle 1, followed by 500 mg once daily for the remaining 28-day cycles. Progression was assessed on the basis of radiographic imaging, rise in carcinoembryonic antigen or lactate dehydrogenase (LDH) levels or by appearance of clinical symptoms. RESULTS: Twenty-eight patients received daily enzastaurin. The 6-month PFS rate was 28% [95% confidence interval (CI) 13%-45%] and median PFS was 1.9 months (95% CI 1.8-4.5 months). Twelve (43%) patients had stable disease with a median duration of 6.1 months. The survival rate at 20 months was 77% (95% CI 47%-92%). No grade 4 toxicity was reported and grade 3 toxic effects were observed in three patients with one patient showing probable drug-related elevation of liver transaminases. CONCLUSION: The window design in asymptomatic patients with mCRC can be safely applied to assess the activity and safety of novel cytostatic agents like enzastaurin.
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| 35. |
- Hajjar, Adeline M, et al.
(författare)
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Lack of in vitro and in vivo recognition of Francisella tularensis subspecies lipopolysaccharide by Toll-like receptors.
- 2006
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Ingår i: Infection and Immunity. - 0019-9567 .- 1098-5522. ; 74:12, s. 6730-8
-
Tidskriftsartikel (refereegranskat)abstract
- Francisella tularensis is an intracellular gram-negative bacterium that is highly infectious and potentially lethal. Several subspecies exist of varying pathogenicity. Infection by only a few organisms is sufficient to cause disease depending on the model system. Lipopolysaccharide (LPS) of gram-negative bacteria is generally recognized by Toll-like receptor 4 (TLR4)/MD-2 and induces a strong proinflammatory response. Examination of human clinical F. tularensis isolates revealed that human virulent type A and type B strains produced lipid A of similar structure to the nonhuman model pathogen of mice, Francisella novicida. F. novicida LPS or lipid A is neither stimulatory nor an antagonist for human and murine cells through TLR4 or TLR2. It does not appear to interact with TLR4 or MD-2, as it is not an antagonist to other stimulatory LPS. Consistent with these observations, aerosolization of F. novicida LPS or whole bacteria induced no inflammatory response in mice. These results suggest that poor innate recognition of F. tularensis allows the bacterium to evade early recognition by the host innate immune system to promote its pathogenesis for mammals.
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| 36. |
- Häussler, Ragna S., et al.
(författare)
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Systematic Development of Sandwich Immunoassays for the Plasma Secretome
- 2019
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Ingår i: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861.
-
Tidskriftsartikel (refereegranskat)abstract
- The plasma proteome offers a clinically useful window into human health. Recent advances from highly multiplexed assays now call for appropriate pipelines to validate individual candidates. Here, a workflow is developed to build dual binder sandwich immunoassays (SIA) and for proteins predicted to be secreted into plasma. Utilizing suspension bead arrays, ≈1800 unique antibody pairs are first screened against 209 proteins with recombinant proteins as well as EDTA plasma. Employing 624 unique antibodies, dilution-dependent curves in plasma and concentration-dependent curves of full-length proteins for 102 (49%) of the targets are obtained. For 22 protein assays, the longitudinal, interindividual, and technical performance is determined in a set of plasma samples collected from 18 healthy subjects every third month over 1 year. Finally, 14 of these assays are compared with with SIAs composed of other binders, proximity extension assays, and affinity-free targeted mass spectrometry. The workflow provides a multiplexed approach to screen for SIA pairs that suggests using at least three antibodies per target. This design is applicable for a wider range of targets of the plasma proteome, and the assays can be applied for discovery but also to validate emerging candidates derived from other platforms.
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| 37. |
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| 38. |
- Karlsborn, Tony, et al.
(författare)
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Elongator, a conserved complex required for wobble uridine modifications in Eukaryotes
- 2014
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Ingår i: RNA Biology. - : Taylor & Francis. - 1547-6286 .- 1555-8584. ; 11:12, s. 1519-1528
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Tidskriftsartikel (refereegranskat)abstract
- Elongator is a 6 subunit protein complex highly conserved in eukaryotes. The role of this complex has been controversial as the pleiotropic phenotypes of Elongator mutants have implicated the complex in several cellular processes. However, in yeast there is convincing evidence that the primary and probably only role of this complex is in formation of the 5-methoxycarbonylmethyl (mcm(5)) and 5-carbamoylmethyl (ncm(5)) side chains on uridines at wobble position in tRNA. In this review we summarize the cellular processes that have been linked to the Elongator complex and discuss its role in tRNA modification and regulation of translation. We also describe additional gene products essential for formation of ncm(5) and mcm(5) side chains at U-34 and their influence on Elongator activity.
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| 39. |
- Karlsborn, Tony, 1987-, et al.
(författare)
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Loss of ncm5 and mcm5 wobble uridine side chains results in an altered metabolic profile
- 2016
-
Ingår i: Metabolomics. - : Springer. - 1573-3882 .- 1573-3890. ; 12:12
-
Tidskriftsartikel (refereegranskat)abstract
- Introduction: The Elongator complex, comprising six subunits (Elp1p-Elp6p), is required for formation of 5-carbamoylmethyl (ncm(5)) and 5-methoxycarbonylmethyl (mcm(5)) side chains on wobble uridines in 11 out of 42 tRNA species in Saccharomyces cerevisiae. Loss of these side chains reduces the efficiency of tRNA decoding during translation, resulting in pleiotropic phenotypes. Overexpression of hypomodified tRNA(s2UUU)(Lys); tRNA(s2UUG)(Gln) and tRNA(s2UUC)(Glu), which in wild-type strains are modified with mcm(5)s(2)U, partially suppress phenotypes of an elp3 Delta strain. Objectives: To identify metabolic alterations in an elp3 Delta strain and elucidate whether these metabolic alterations are suppressed by overexpression of hypomodified tRNA(s2UUU)(Lys); tRNA(s2UUG)(Gln) and tRNA(s2UUC)(Glu). Method: Metabolic profiles were obtained using untargeted GC-TOF-MS of a temperature-sensitive elp3 Delta strain carrying either an empty low-copy vector, an empty high-copy vector, a low-copy vector harboring the wild-type ELP3 gene, or a high-copy vector overexpressing tRNA(s2UUU)(Lys); tRNA(s2UUG)(Gln) and tRNA(s2UUC)(Glu). The temperature sensitive elp3 Delta strain derivatives were cultivated at permissive (30 degrees C) or semi-permissive (34 degrees C) growth conditions. Results: Culturing an elp3 Delta strain at 30 or 34 degrees C resulted in altered metabolism of 36 and 46 %, respectively, of all metabolites detected when compared to an elp3D strain carrying the wild-type ELP3 gene. Overexpression of hypomodified tRNA(s2UUU)(Lys); tRNA(s2UUG)(Gln) and tRNA(s2UUC)(Glu) suppressed a subset of the metabolic alterations observed in the elp3 Delta strain. Conclusion: Our results suggest that the presence of ncm(5)- and mcm(5)-side chains on wobble uridines in tRNA are important for metabolic homeostasis.
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| 40. |
- Macari, F., et al.
(författare)
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TRM6/61 connects PKCα with translational control through tRNAiMet stabilization : impact on tumorigenesis
- 2016
-
Ingår i: Oncogene. - : Springer Science and Business Media LLC. - 0950-9232 .- 1476-5594. ; 35:14, s. 1785-1796
-
Tidskriftsartikel (refereegranskat)abstract
- Accumulating evidence suggests that changes of the protein synthesis machinery alter translation of specific mRNAs and participate in malignant transformation. Here we show that protein kinase C [alpha] (PKC[alpha]) interacts with TRM61, the catalytic subunit of the TRM6/61 tRNA methyltransferase. The TRM6/61 complex is known to methylate the adenosine 58 of the initiator methionine tRNA (tRNAiMet), a nuclear post-transcriptional modification associated with the stabilization of this crucial component of the translation-initiation process. Depletion of TRM6/61 reduced proliferation and increased death of C6 glioma cells, effects that can be partially rescued by overexpression of tRNAiMet. In contrast, elevated TRM6/61 expression regulated the translation of a subset of mRNAs encoding proteins involved in the tumorigenic process and increased the ability of C6 cells to form colonies in soft agar or spheres when grown in suspension. In TRM6/61/tRNAiMet-overexpressing cells, PKC[alpha] overexpression decreased tRNAiMet expression and both colony- and sphere-forming potentials. A concomitant increase in TRM6/TRM61 mRNA and tRNAiMet expression with decreased expression of PKC[alpha] mRNA was detected in highly aggressive glioblastoma multiforme as compared with Grade II/III glioblastomas, highlighting the clinical relevance of our findings. Altogether, we suggest that PKC[alpha] tightly controls TRM6/61 activity to prevent translation deregulation that would favor neoplastic development.
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| 41. |
- Macura, Biljana, et al.
(författare)
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What is the impact on fish recruitment of anthropogenic physical and structural habitat change in shallow nearshore areas in temperate systems? : A systematic review protocol
- 2016
-
Ingår i: Environmental Evidence. - : Springer Science and Business Media LLC. - 2047-2382. ; 5:1
-
Forskningsöversikt (refereegranskat)abstract
- Background:Shallow nearshore marine ecosystems are changing at an increasing rate due to a range of human activities such as urbanisation and commercial development. The growing numbers of constructions and other physical and structural alterations of the shoreline often take place in nursery and spawning habitats of many fish and other aquatic species. Several coastal fish populations have seen marked declines in abundance and diversity during the past two decades. A systematic review on the topic would clarify if anthropogenic physical and structural changes of near-shore areas have effects on fish recruitment and which these effects are.Methods:The review will examine how various physical and structural anthropogenic changes of nearshore fish habitats affect fish recruitment. Relevant studies include small- and large-scale field studies in marine and brackish systems or large lakes in temperate regions of the Northern and Southern hemispheres. Relevant studies may be based on comparisons between undisturbed and disturbed areas, before and after disturbance, or both. Relevant outcomes include measures of recruitment defined as abundance of juveniles of nearshore fish communities. Searches will be made for peer-reviewed and grey literature in English, Dutch, Danish, Finnish, German, Swedish and Spanish. All fish species and species groups will be considered in this review. Included relevant studies will be subject to a critical appraisal that will assess study validity. From relevant included studies, we will extract information on study characteristics, measured outcomes, exposure, comparators, effect modifiers and critical appraisal. Data synthesis will contain narrative and summary findings of each included study of sufficient quality. Meta-analysis may be possible in cases where studies report similar types of outcomes.
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| 42. |
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| 43. |
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| 44. |
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| 45. |
- Persson, Lennart, et al.
(författare)
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Cannibalism in a size-structured population : energy extraction and control
- 2004
-
Ingår i: Ecological Monographs. - : Wiley. - 0012-9615 .- 1557-7015. ; 74:1, s. 135-157
-
Tidskriftsartikel (refereegranskat)abstract
- Recent size-structured cannibalistic models point to the importance of the energy gain by cannibals and also show that this gain may result in the emergence of giant individuals. We use a combination of a 10-year field study of a perch (Perca fluviatilis) population and quantitative within-season modeling of individual and population-level dynamics to investigate which mechanisms are most likely to drive the dynamics of the studied perch population. We focused on three main aspects to explain observed discrepancies between earlier model predictions and data: (1) introduction of more than one shared resource between cannibals and victims, (2) whether or not several victim age cohorts are necessary to allow giant growth, and (3) the intensity of inter-cohort competition between young-of-the-year (YOY) perch and 1-yr-old perch. At the start of the study period, the perch population was dominated by “stunted” perch individuals, and recruitment of perch to an age of 1-yr-old was negligible. Following a major death in adult perch, strong recruitments of perch to 1-yr-old were thereafter observed for a number of years. As 1-yr-olds these successful recruiters subsequently starved to death due to competition with the new YOY. The few surviving adult perch accelerated substantially in growth and became “giants.” At the end of the study period, the perch population moved back to the situation with stunted individuals. There was a high agreement between observed diets of cannibalistic perch and those predicted by the model for both the stunted and the giant phases. Analyses of growth rates showed that cannibalistic perch could become giants on a diet of YOY perch only, but that a supplement with the second shared resource (macroinvertebrates) was needed to reach the observed sizes. Modeling of growth and diet in the giant phase showed an exploitative competitive effect of YOY perch on 1-yr-old perch, but a restriction in habitat use of 1-yr-old perch had to be assumed to yield the observed growth rate and diet. The resource dynamics of zooplankton and macroinvertebrates were both accurately predicted by the model. Also, YOY perch mortality was accurately predicted and, furthermore, suggested that one of the trawling methods used may underestimate the number of YOY perch when they increase in size. We conclude that the presence of a second shared resource and the restricted habitat use and absence of cannibalistic consumption by 1-yr-old perch individuals are two important mechanisms to explain the discrepancy between model predictions and data. Our results also point to the fact that that the dynamics observed may be explained by complex dynamics not involving the presence of a giant and dwarf cycle.
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| 46. |
- Persson, Lennart, et al.
(författare)
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State-dependent invasion windows for prey in size-structured predator–prey systems: whole lake experiments
- 2007
-
Ingår i: Journal of Animal Ecology. - : Wiley. - 0021-8790 .- 1365-2656. ; 76:1, s. 94-104
-
Tidskriftsartikel (refereegranskat)abstract
- 1.In size-structured communities where individuals grow in size over their life cycle, interactions between species will shift between competitive and predatory interactions depending on size relationships. The outcome of interactions will subsequently depend on the strength of competitive and predatory interactions, respectively.2.In a whole lake experiment including four experimental lakes, it was tested under which conditions the competing prey, roach Rutilus rutilus, could successfully recruit into systems previously occupied by the predator, perch Perca fluviatilis. Two replicated introduction experiments were carried out 3 years apart.3.Roach were able to successfully recruit into three of the four experimental lakes of which two were also inhabited by the top predator pike Esox lucius. Resource levels were unrelated to whether roach could successfully recruit into the systems as recruiting roach in all years were feeding close to their maximum rate.4.High population fecundity of roach and low predation pressure by perch combined were necessary ingredients for successful recruitment and the presence of only one of these conditions did not result in successful recruitment.5.It is hypothesized that, although roach were able to successfully recruit into one lake with only perch present in addition to the two lakes that also inhabited pike, long-term coexistence of roach and perch depends on the presence of another top predator (e.g. pike) selectively preying on perch. This hypothesis was supported by data on co-occurrence of perch and roach in different lakes.6.Overall, the results are in accordance with expectation of size-structured life-history omnivory theory suggesting that coexistence between top predator and intermediate consumer is fragile.
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| 47. |
- Persson-Sjodin, Emma, et al.
(författare)
-
Withers vertical movement symmetry is useful for locating the primary lame limb in naturally occurring lameness
- 2024
-
Ingår i: Equine Veterinary Journal. - : WILEY. - 0425-1644 .- 2042-3306. ; 56:1, s. 76-88
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundDuring orthopaedic assessment of lame horses, a head nod is commonly present in both primary forelimb and hindlimb lame horses. Additional motion metrics that could assist clinicians in correctly differentiating between these two scenarios would be of great clinical value. ObjectivesThe primary objective of this study was to examine whether withers movement asymmetry can be used in a clinical setting to distinguish primary forelimb lameness from compensatory head movement asymmetry due to primary hindlimb lameness. Study designRetrospective, multicentre study. MethodsMovement asymmetry of head, withers and pelvis was measured using multi-camera optical motion capture, as part of routine lameness investigations at four European equine hospitals. Vertical movement asymmetry parameters from 317 horses trotting in a straight line were compared before and after successful diagnostic analgesia of a single limb. Descriptive statistics, t-tests and linear models were used to analyse the data. ResultsIn forelimb lame horses, 80%-81% showed head and withers asymmetry both indicating lameness in the same forelimb. In hindlimb lame horses, 69%-72% showed head asymmetry ipsilateral to the lame hindlimb and withers asymmetry diagonal to the lame hindlimb, thus, head and withers asymmetry indicated lameness in different forelimbs. A large (>15 mm) compensatory head nod was seen in 28%-31% of the hindlimb lame horses. In 89%-92% of these, head and withers asymmetry indicated lameness in different forelimbs. Withers asymmetry decreased linearly with reduced head or pelvic asymmetry for both forelimb and hindlimb lame horses. Main limitationsCompensatory strategies were evaluated on group level to identify common patterns, potentially ignoring uncommon individual strategies. ConclusionsWithers vertical movement asymmetry metrics can be useful in helping to locate the primary lame limb during quantitative lameness assessment. Head and withers movement asymmetry parameters generally indicate the same forelimb in forelimb lame horses, but different forelimbs in hindlimb lame horses.
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| 48. |
- Pettersson, B. M. Fredrik, 1974-
(författare)
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tRNA Gene Structures in Bacteria
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In bacteria, tRNA molecules are produced as precursors with additional nucleotides both upstream and downstream of the tRNA coding sequence. To generate a mature tRNA, the endoribonuclease RNase P removes the upstream sequence, while a number of enzymes can remove the downstream sequence. In this thesis, the influence of such upstream and downstream sequences on the expression of mature functional tRNA was studied. It was found that in Escherichia coli, the presence of an upstream sequence positively influences tRNA expression. Furthermore, it was shown that the identity of the nucleotide immediatedly 5' of the canonical RNase P cleavage site in a tRNA precursor influenced RNase P cleavage site selection in vivo in E. coli, but not in Pseudomonas aeruginosa. Additionally, a stem-loop in the precursor just downstream of the tRNA increased this "miscleavage". This stem-loop resembled a rho-independent transcription terminator and overlapped the trpT gene in P. aeruginosa, but it only marginally influenced the expression of the downstream secE gene. The trpT and secE genes were found to be cotranscribed. The trpT-secE gene order was also conserved in the majority of bacteria investigated. The expression of tRNA genes during development in Streptomyces coelicolor was also studied. Here, the expression of most tRNA genes tested increased with time during development. Similarly, the expression of the RNase P RNA increased. The relative increase was quantified and correlated with different criteria related to gene structure and gene organisation, but no significant differences could be found. Moreover, a tRNALeuCAA UUA codon suppressor as well as the cognate bldA tRNA could restore differentiation to a developmentally blocked bldA deletion strain. For both tRNAs, the efficiency of restoration depended on the 5'- and 3'-flanks. In conclusion, both 5'- and 3'-flanking sequences influence tRNA expression, and bacteria respond differently to changes in their tRNA gene structures.
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| 49. |
- Piispanen, PS, et al.
(författare)
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Synthesis and characterization of surface-active compounds derived from cholesterol derivatives and glucose
- 2002
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Ingår i: Journal of Surfactants and Detergents (JSD). - 1097-3958 .- 1558-9293. ; 5, s. 345-351
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Tidskriftsartikel (refereegranskat)abstract
- The synthesis and characterization of surface-active compounds based on various steroid derivatives and glucose are presented. The hydrophobic and hydrophilic parts of the compounds were linked via glucosidic bonds. All compounds were found to have very low water solubility and only limited solubility in various organic solvents. The compounds were investigated according to their ability to interact with an anionic surfactant, sodium dodecylsulfate (SDS), in order to induce a decrease in the critical micelle concentration (CMC) of the surfactants. This synergistic effect was pronounced for cholestanol-6-on-ß-d-glucopyranoside and for cholestan-3,6-diol-ß-d-glucopyranoside. These two compounds lowered the CMC from 8 to 6 and 0.6 mM, respectively, for water solutions of SDS/glucoside with a molar ratio of 92:8. Furthermore, the ability of the compounds to stabilize lipid membranes, in liposomes, at varying concentrations of Ca2+, was studied. The compounds were, as expected, found to induce stabilization similar to that of cholesterol
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| 50. |
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