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- Bergström, Petra, et al.
(author)
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Association of NFE2L2 and KEAP1 haplotypes with amyotrophic lateral sclerosis.
- 2014
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In: Amyotrophic lateral sclerosis & frontotemporal degeneration. - : Informa UK Limited. - 2167-9223 .- 2167-8421. ; 15:1-2, s. 130-137
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Journal article (peer-reviewed)abstract
- Amyotrophic lateral sclerosis (ALS) is a degenerative motor neuron syndrome influenced by oxidative stress. The transcription factor Nrf2 and its repressor Keap1 constitute an important defence system in cellular protection against oxidative stress. Here we hypothesize that common genetic variations in the genes NFE2L2 and KEAP1, encoding Nrf2 and Keap1, may influence the risk and phenotype of ALS. Five hundred and twenty-two Swedish patients with sporadic ALS (SALS) and 564 Swedish control subjects were studied. Eight tag SNPs in NFE2L2 and three tag SNPs in KEAP1 were genotyped by allelic discrimination and three functional NFE2L2 promoter SNPs were genotyped by sequencing. One NFE2L2 haplotype (GGGAC) was associated with decreased risk of SALS (OR = 0.62 per allele, p = 0.003) and one haplotype in KEAP1 (CGG) was associated with later SALS onset (+3.4 years per allele, p = 0.015). When stratified by subgroup, one haplotype in NFE2L2, GAGCAGA including three functional promoter SNPs associated with high Nrf2 protein expression, was associated with 4.0 years later disease onset per allele in subgroup ALS (p = 0.008). In conclusion, these results suggest that variations in NFE2L2 and KEAP1, encoding two central proteins in cellular oxidative stress defence, may influence SALS pathogenesis.
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| 2. |
- Einarsdottir, Berglind Osk, 1979, et al.
(author)
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Melanoma patient-derived xenografts accurately model the disease and develop fast enough to guide treatment decisions.
- 2014
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In: Oncotarget. - : Impact Journals, LLC. - 1949-2553. ; 5:20, s. 9609-18
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Journal article (peer-reviewed)abstract
- The development of novel therapies against melanoma would benefit from individualized tumor models to ensure the rapid and accurate identification of biomarkers of therapy response. Previous studies have suggested that patient-derived xenografts (PDXes) could be useful. However, the utility of PDXes in guiding real-time treatment decisions has only been reported in anecdotal forms. Here tumor biopsies from patients with stage III and IV metastatic malignant melanoma were transplanted into immunocompromised mice to generate PDXes. 23/26 melanoma biopsies generated serially transplantable PDX models, and their histology, mutation status and expression profile resembled their corresponding patient biopsy. The potential treatment for one patient was revealed by an in vitro drug screen and treating PDXes with the MEK inhibitor trametinib. In another patient, the BRAF mutation predicted the response of both the patient and its corresponding PDXes to MAPK-targeted therapy. Importantly, in this unselected group of patients, the time from biopsy for generation of PDXes until death was significantly longer than the time required to reach the treatment phase of the PDXes. Thus, it could be clinically meaningful to use this type of platform for melanoma patients as a pre-selection tool in clinical trials.
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| 3. |
- Nilsson, Magnus, et al.
(author)
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A 9-band WCDMA/EDGE transceiver supporting HSPA evolution
- 2011
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In: [Host publication title missing]. - 0193-6530. ; , s. 366-368
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Conference paper (peer-reviewed)abstract
- The future of cellular radio ICs lies in the integration of an ever-increasing number of bands and channel bandwidths. This paper presents a transceiver together with the associated discrete front-end components. The transceiver supports 4 EDGE bands and 9 WCDMA bands (l-VI and Vlll-X), while the radio can be configured to simultaneously support the 4 EDGE bands and up to 5 WCDMA bands: 3 high bands (HB) and 2 low bands (LB). The RX is a SAW-less homodyne composed of a main RX and a diversity RX. To reduce package complexity with so many bands, we chose to minimize the number of ports by using single-ended RF interfaces for both RX and TX. This saves seve ral package pins, but requires careful attention to grounding. The main RX has 8 LNA ports and the diversity RX has 5, with some LNAs supporting multiple bands. On the TX side, 2 ports are used for all EDGE bands and 4 for the WCDMA bands.
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| 6. |
- Abarenkov, Kessy, et al.
(author)
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PlutoF—a web based workbench for ecological and taxonomic research, with an online implementation for fungal ITS sequences
- 2010
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In: Evolutionary Bioinformatics. - 1176-9343. ; 6, s. 189-196
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Journal article (peer-reviewed)abstract
- DNA sequences accumulating in the International Nucleotide Sequence Databases (INSD) form a rich source of information for taxonomic and ecological meta-analyses. However, these databases include many erroneous entries, and the data itself is poorly annotated with metadata, making it difficult to target and extract entries of interest with any degree of precision. Here we describe the web-based workbench PlutoF, which is designed to bridge the gap between the needs of contemporary research in biology and the existing software resources and databases. Built on a relational database, PlutoF allows remote-access rapid submission, retrieval, and analysis of study, specimen, and sequence data in INSD as well as for private datasets though web-based thin clients. In contrast to INSD, PlutoF supports internationally standardized terminology to allow very specific annotation and linking of interacting specimens and species. The sequence analysis module is optimized for identification and analysis of environmental ITS sequences of fungi, but it can be modified to operate on any genetic marker and group of organisms. The workbench is available at http://plutof.ut.ee.
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| 9. |
- Annerbrink, Kristina, 1974, et al.
(author)
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Associations between the angiotensin-converting enzyme insertion/deletion polymorphism and monoamine metabolite concentrations in cerebrospinal fluid
- 2010
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In: Psychiatry Research. - : Elsevier BV. - 1872-7123 .- 0165-1781. ; 179:2, s. 231-234
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Journal article (peer-reviewed)abstract
- Angiotensin II has been suggested to influence central dopamine and serotonin turnover. Since the angiotensin-converting enzyme (ACE) plays a key role in angiotensin regulation by converting inactive angiotensin 1 to active angiotensin II, we hypothesised that the functional insertion/deletion (I/D) polymorphism in the ACE gene, which has previously been suggested to be associated with, depression and panic disorder, may influence monoamine activity. A well-established technique for assessing brain monoamine turnover in humans is to measure concentrations of monoamine metabolites in the cerebrospinal fluid (CSF). We thus investigated possible associations between the ACE I/D polymorphism and CSF monoamine metabolite concentrations in a population of healthy male subjects. After having found such an association between the ACE I/D polymorphism and CSF levels of the dopamine metabolite homovanillic acid and the serotonin metabolite 5-hydroxyindoleacetic acid in this sample, I carriers displaying lower levels, we tried to replicate this observation in a population of violent male offenders from which also both CSF and DNA were available. Also in this sample, the same associations were found. Our results suggest that the ACE I/D polymorphism may play a role in the modulation of serotonergic and dopaminergic turnover in men. (C) 2009 Elsevier Ireland Ltd. All rights reserved.
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| 10. |
- Antonelli, Alexandre, 1978, et al.
(author)
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SUPERSMART: ecology and evolution in the era of big data
- 2014
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In: PeerJ PrePrints. - : PeerJ. - 2167-9843.
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Journal article (other academic/artistic)abstract
- Rapidly growing biological data volumes – including molecular sequences, species traits, geographic occurrences, specimen collections, and fossil records – hold an unprecedented, yet largely unexplored potential to reveal how ecological and evolutionary processes generate and maintain biodiversity. Most biodiversity studies integrating ecological data and evolutionary history use an idiosyncratic step-by-step approach for the reconstruction of time-calibrated phylogenies in light of ecological and evolutionary scenarios. Here we introduce a conceptual framework, termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of biodiversity research. This framework reconstructs dated phylogenies based on the assembly of molecular datasets and collects pertinent data on ecology, distribution, and fossils of the focal clade. The data handled for each step are continuously updated as databases accumulate new records. We exemplify the practice of our method by presenting comprehensive phylogenetic and dating analyses for the orders Primates and the Gentianales. We believe that this emerging framework will provide an invaluable tool for a wide range of hypothesis-driven research questions in ecology and evolution.
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