| 1. |
- Elsik, Christine G., et al.
(author)
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The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
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Journal article (peer-reviewed)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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| 2. |
- Armitage, James M, et al.
(author)
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Modeling the Global Fate and Transport of Perfluorooctane Sulfonate (PFOS) and Precursor Compounds in Relation to Temporal Trends in Wildlife Exposure.
- 2009
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In: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 43:24, s. 9274-80
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Journal article (peer-reviewed)abstract
- A global-scale fate and transport model was applied to investigate the historic and future trends in ambient concentrations of perfluorooctane sulfonate (PFOS) and volatile perfluorooctane sulfonyl fluoride (POSF)-based precursor compounds in the environment. First, a global emission inventory for PFOS and its precursor compounds was estimated for the period 1957-2010. We used this inventory as input to a global-scale contaminant fate model and compared modeled concentrations with field data. The main focus of the simulations was to examine how modeled concentrations of PFOS and volatile precursor compounds respond to the major production phase-out that occurred in 2000-2002. Modeled concentrations of PFOS in surface ocean waters are generally within a factor of 5 of field data and are dominated by direct emissions of this substance. In contrast, modeled concentrations of the precursor compounds considered in this study are lower than measured concentrations both before and after the production phase-out. Modeled surface ocean water concentrations of PFOS in source regions decline slowly in response to the production phase-out while concentrations in remote regions continue to increase until 2030. In contrast, modeled concentrations of precursor compounds in both the atmosphere and surface ocean water compartment in all regions respond rapidly to the production phase-out (i.e., decline quickly to much lower levels). With respect to wildlife biomonitoring data, since precursor compounds are bioavailable and degrade to PFOS in vivo, it is at least plausible that declining trends in PFOS body burdens observed in some marine organisms are attributable to this exposure pathway. The continued increases in PFOS body burdens observed in marine organisms inhabiting other regions may reflect exposure primarily to PFOS itself, present in the environment due to production and use of this compound as well as degradation of precursor compounds.
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| 3. |
- Birney, Ewan, et al.
(author)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Journal article (peer-reviewed)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 4. |
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| 5. |
- Butler, Geraldine, et al.
(author)
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Evolution of pathogenicity and sexual reproduction in eight Candida genomes.
- 2009
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 459:7247, s. 657-62
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Journal article (peer-reviewed)abstract
- Candida species are the most common cause of opportunistic fungal infection worldwide. Here we report the genome sequences of six Candida species and compare these and related pathogens and non-pathogens. There are significant expansions of cell wall, secreted and transporter gene families in pathogenic species, suggesting adaptations associated with virulence. Large genomic tracts are homozygous in three diploid species, possibly resulting from recent recombination events. Surprisingly, key components of the mating and meiosis pathways are missing from several species. These include major differences at the mating-type loci (MTL); Lodderomyces elongisporus lacks MTL, and components of the a1/2 cell identity determinant were lost in other species, raising questions about how mating and cell types are controlled. Analysis of the CUG leucine-to-serine genetic-code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the Candida albicans gene catalogue, identifying many new genes.
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| 6. |
- Willer, Cristen J., et al.
(author)
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Six new loci associated with body mass index highlight a neuronal influence on body weight regulation
- 2009
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 41:1, s. 25-34
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Journal article (peer-reviewed)abstract
- Common variants at only two loci, FTO and MC4R, have been reproducibly associated with body mass index (BMI) in humans. To identify additional loci, we conducted meta-analysis of 15 genome-wide association studies for BMI (n > 32,000) and followed up top signals in 14 additional cohorts (n > 59,000). We strongly confirm FTO and MC4R and identify six additional loci (P < 5 x 10(-8)): TMEM18, KCTD15, GNPDA2, SH2B1, MTCH2 and NEGR1 (where a 45-kb deletion polymorphism is a candidate causal variant). Several of the likely causal genes are highly expressed or known to act in the central nervous system (CNS), emphasizing, as in rare monogenic forms of obesity, the role of the CNS in predisposition to obesity.
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| 7. |
- Willerslev, Eske, et al.
(author)
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Ancient biomolecules from deep ice cores reveal a forested Southern Greenland
- 2007
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In: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 317:5834, s. 111-114
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Journal article (peer-reviewed)abstract
- It is difficult to obtain fossil data from the 10% of Earth's terrestrial surface that is covered by thick glaciers and ice sheets, and hence, knowledge of the paleoenvironments of these regions has remained limited. We show that DNA and amino acids from buried organisms can be recovered from the basal sections of deep ice cores, enabling reconstructions of past flora and fauna. We show that high-altitude southern Greenland, currently lying below more than 2 kilometers of ice, was inhabited by a diverse array of conifer trees and insects within the past million years. The results provide direct evidence in support of a forested southern Greenland and suggest that many deep ice cores may contain genetic records of paleoenvironments in their basal sections.
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| 8. |
- Aksentijevich, Ivona, et al.
(author)
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An Autoinflammatory Disease with Deficiency of the Interleukin-1-Receptor Antagonist
- 2009
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In: New England Journal of Medicine. - 0028-4793. ; 360:23, s. 2426-2437
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Journal article (peer-reviewed)abstract
- BACKGROUND Autoinflammatory diseases manifest inflammation without evidence of infection, high-titer autoantibodies, or autoreactive T cells. We report a disorder caused by mutations of IL1RN, which encodes the interleukin-1-receptor antagonist, with prominent involvement of skin and bone. METHODS We studied nine children from six families who had neonatal onset of sterile multifocal osteomyelitis, periostitis, and pustulosis. Response to empirical treatment with the recombinant interleukin-1-receptor antagonist anakinra in the first patient prompted us to test for the presence of mutations and changes in proteins and their function in interleukin-1-pathway genes including IL1RN. RESULTS We identified homozygous mutations of IL1RN in nine affected children, from one family from Newfoundland, Canada, three families from the Netherlands, and one consanguineous family from Lebanon. A nonconsanguineous patient from Puerto Rico was homozygous for a genomic deletion that includes IL1RN and five other interleukin-1-family members. At least three of the mutations are founder mutations; heterozygous carriers were asymptomatic, with no cytokine abnormalities in vitro. The IL1RN mutations resulted in a truncated protein that is not secreted, thereby rendering cells hyperresponsive to interleukin-1 beta stimulation. Patients treated with anakinra responded rapidly. CONCLUSIONS We propose the term deficiency of the interleukin-1-receptor antagonist, or DIRA, to denote this autosomal recessive autoinflammatory disease caused by mutations affecting IL1RN. The absence of interleukin-1-receptor antagonist allows unopposed action of interleukin-1, resulting in life-threatening systemic inflammation with skin and bone involvement. (ClinicalTrials.gov number, NCT00059748.)
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| 9. |
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| 10. |
- Buckingham, Matthew, et al.
(author)
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Matthew Buckingham
- 2007
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In: Historielärarnas Förenings Årsskrift. - 0439-2434.
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Journal article (peer-reviewed)
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| 11. |
- Byröd, Martin, et al.
(author)
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Minimal Solutions for Panoramic Stitching with Radial Distortion
- 2009
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In: British Machine Vision Conference.
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Conference paper (peer-reviewed)abstract
- This paper presents a solution to panoramic image stitching of two images with co- inciding optical centers, but unknown focal length and radial distortion. The algorithm operates with a minimal set of corresponding points (three) which means that it is well suited for use in any RANSAC style algorithm for simultaneous estimation of geometry and outlier rejection. Compared to a previous method for this problem, we are able to guarantee that the right solution is found in all cases. The solution is obtained by solving a small system of polynomial equations. The proposed algorithm has been integrated in a complete multi image stitching system and we evaluate its performance on real images with lens distortion. We demonstrate both quantitative and qualitative improvements compared to state of the art methods.
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| 12. |
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| 13. |
- Hell, Martin, et al.
(author)
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The Grain family of stream ciphers
- 2008
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In: New Stream Cipher Designs - The eSTREAM Finalists. - 0302-9743 .- 1611-3349. - 9783540683506 ; , s. 179-190
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Book chapter (peer-reviewed)abstract
- Abstract in UndeterminedA new family of stream ciphers, Grain, is proposed. Two variants, a 80-bit and a 128-bit variant are specified, denoted Grain and Grain-128 respectively. The designs target hardware environments where gate count, power consumption and memory are very limited. Both variants are based on two shift registers and a nonlinear output function. The ciphers also have the additional feature that the speed can be easily increased at the expense of extra hardware.
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| 14. |
- Ingelsson, Martin, et al.
(author)
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Increase in the relative expression of tau with four microtubule binding repeat regions in frontotemporal lobar degeneration and progressive supranuclear palsy brains
- 2007
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In: Acta Neuropathologica. - : Springer Science and Business Media LLC. - 0001-6322 .- 1432-0533. ; 114:5, s. 471-479
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Journal article (peer-reviewed)abstract
- Some cases of familial frontotemporal dementia (FTD) leading to frontotemporal lobar degeneration (FTLD) are caused by mutations in tau on chromosome 17 (FTDP-17). Certain mutations alter the ratio between four (4R tau) and three (3R tau) repeat tau isoforms whereas cases with progressive supranuclear palsy (PSP) and corticobasal degeneration (CBD) mainly have 4R tau brain pathology. We assessed tau mRNA and protein levels in frontal cortex from 15 sporadic FTLD, 21 PSP, 5 CBD, 15 Alzheimer’s disease (AD) and 16 control brains. Moreover, we investigated the disease association and possible tau splicing effects of the tau H1 haplotype. Cases with FTLD and PSP had lower tau mRNA levels than control brains. When analyzing 4R tau and 3R tau mRNA separately, control subjects displayed a 4R tau/3R tau ratio of 0.48. Surprisingly, FTLD brains displayed a more elevated ratio (1.32) than PSP brains (1.12). Also, several FTLD and PSP cases had higher 4R tau/3R tau mRNA than FTDP-17 cases, included as reference tissues, and the ratio increase was seen regardless of underlying histopathology, i.e. both for tau-positive and tau-negative FTLD cases. Furthermore, total tau protein levels were slightly decreased in both FTLD and AD as compared to control subjects. Finally, we confirmed the association of tau H1 with PSP, but could not find any haplotype-related effect on tau exon 10 splicing. In conclusion, we demonstrated increased but largely variable 4R tau/3R tau mRNA ratios in FTLD and PSP cases, suggesting heterogeneous pathophysiological processes within these disorders.
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| 15. |
- Ingelsson, Martin, et al.
(author)
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No alteration in tau exon 10 alternative splicing in tangle-bearing neurons of the Alzheimer's disease brain
- 2006
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In: Acta Neuropathologica. - : Springer Science and Business Media LLC. - 0001-6322 .- 1432-0533. ; 112:4, s. 439-449
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Journal article (peer-reviewed)abstract
- Defective splicing of tau mRNA, promoting a shift between tau isoforms with (4R tau) and without (3R tau) exon 10, is believed to be a pathological consequence of certain tau mutations causing frontotemporal dementia. By assessing protein and mRNA levels of 4R tau and 3R tau in 27 AD and 20 control temporal cortex, we investigated whether altered tau splicing is a feature also in Alzheimer's disease (AD). However, apart from an expected increase of sarcosyl-insoluble tau in AD, there were no significant differences between the groups. Next, by laser-capture microscopy and quantitative PCR, we separately analyzed CA1 hippocampal neurons with and without neurofibrillary pathology from six of the AD and seven of the control brains. No statistically significant differences in 4R tau/3R tau mRNA were found between the different subgroups. Moreover, we confirmed the absence of significant ratio differences in a second data set with laser-captured entorhinal cortex neurons from four AD and four control brains. Finally, the 4R tau/3R tau ratio in CA1 neurons was roughly half of the ratio in temporal cortex, indicating region-specific differences in tau mRNA splicing. In conclusion, this study indicated region-specific and possibly cell-type-specific tau splicing but did not lend any support to overt changes in alternative splicing of tau exon 10 being an underlying factor in AD pathogenesis.
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| 16. |
- Matsui, Toshifumi, et al.
(author)
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Expression of APP pathway mRNAs and proteins in Alzheimer's disease
- 2007
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In: Brain Research. - : Elsevier BV. - 0006-8993 .- 1872-6240. ; 1161, s. 116-123
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Journal article (peer-reviewed)abstract
- In both trisomy 21 and rare cases of triplication of amyloid precursor protein (APP) Alzheimer's disease (AD) pathological changes are believed to be secondary to increased expression of APP. We hypothesized that sporadic AD may also be associated with changes in transcription of APP or its metabolic partners. To address this issue, temporal neocortex of 27 AD and 21 non-demented control brains was examined to assess mRNA levels of APP isoforms (total APP, APP containing the Kunitz protease inhibitor domain [APP-KPI] and APP770) and APP metabolic enzymatic partners (the APP cleaving enzymes beta-secretase [BACE] and presenilin-1 [PS- 1], and putative clearance molecules, low-density lipoprotein receptor protein [LRP] and apolipoprotein E [apoE]). Furthermore, we evaluated how changes in APP at the mRNA level affect the amount of Tris buffer extractable APP protein and A beta 40 and 42 peptides in AD and control brains. As assessed by quantitative PCR, APP-KPI (p=0.007), APP770 (p=0.004), PS-1 (p = 0.004), LRP (p = 0.003), apoE (p = 0.0002) and GFAP (p < 0.0001) mRNA levels all increased in AD, and there was a shift from APP695 (a neuronal isoform) towards KPI containing isoforms that are present in glia as well. APP-KPI mRNA levels correlated with soluble APP alpha -KPI protein (sAPP alpha -KPI) levels measured by ELISA (T= 0.33, p = 0.015 by Kendall's rank correlation); in turn, soluble APP alpha-KPI protein levels positively correlated with Tris -extractable, soluble A beta 40 (p=0.046) and 42 levels (p=0.007). The ratio of soluble APP alpha-KPI protein levels to total APP protein increased in AD, and also correlated with GFAP protein levels in AD. These results suggest that altered transcription of APP in AD is proportionately associated with A beta peptide, may occur in the context of gliosis, and may contribute to A beta deposition in sporadic AD.
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| 17. |
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| 18. |
- Peacock, Christopher S, et al.
(author)
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Comparative genomic analysis of three Leishmania species that cause diverse human disease.
- 2007
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 39:7, s. 839-847
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Journal article (peer-reviewed)abstract
- Leishmania parasites cause a broad spectrum of clinical disease. Here we report the sequencing of the genomes of two species of Leishmania: Leishmania infantum and Leishmania braziliensis. The comparison of these sequences with the published genome of Leishmania major reveals marked conservation of synteny and identifies only 200 genes with a differential distribution between the three species. L. braziliensis, contrary to Leishmania species examined so far, possesses components of a putative RNA-mediated interference pathway, telomere-associated transposable elements and spliced leader–associated SLACS retrotransposons. We show that pseudogene formation and gene loss are the principal forces shaping the different genomes. Genes that are differentially distributed between the species encode proteins implicated in host-pathogen interactions and parasite survival in the macrophage.
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| 19. |
- Skoglund, Lena, et al.
(author)
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No evidence of PGRN or MAPT gene dosage alterations in a collection of patients with frontotemporal lobar degeneration
- 2009
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In: Dementia and Geriatric Cognitive Disorders. - : S. Karger AG. - 1420-8008 .- 1421-9824. ; 28:5, s. 471-475
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Journal article (peer-reviewed)abstract
- Background/Aims Alterations in gene dosage have recently been associated with neurodegenerative disorders, such as Alzheimer's disease and Parkinson's disease, and deletions of the progranulin (PGRN) locus were recently described in patients with frontotemporal lobar degeneration (FTLD). FTLD is a genetically complex neurodegenerative disorder with mutations in the PGRN and the microtubule-associated protein tau (MAPT) genes being the most common known causes of familial FTLD. In this study, we investigated 39 patients with FTLD, previously found negative for mutations in PGRN and MAPT, for copy number alterations of these 2 genes. Methods Gene dosage analysis of PGRN and MAPT was performed using multiplex ligation-dependent probe amplification. Results We did not identify any PGRN or MAPT gene dosage variations in the 39 FTLD patients investigated. Conclusion We therefore conclude that alterations in gene copy number of PGRN and MAPT are not a cause of disease in this ollection of FTLD patients.
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| 20. |
- Slama, Jiri, et al.
(author)
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Plesovice zircon : A new natural reference material for U-Pb and Hf isotopic microanalysis
- 2008
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In: Chemical Geology. - : Elsevier BV. - 0009-2541 .- 1872-6836. ; 249:02-jan, s. 1-35
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Journal article (peer-reviewed)abstract
- Matrix-matched calibration by natural zircon standards and analysis of natural materials as a reference are the principle methods for achieving accurate results in inicrobeam U-Pb dating and Hf isotopic analysis. We describe a new potential zircon reference material for laser ablation ICP-MS that was extracted from a potassic granulite facies rock collected in the southern part of the Bohemian Massif (Plesovice, Czech Republic). Data from different techniques (ID-TIMS, SIMS and LA ICP-MS) and several laboratories suggest that this zircon has a concordant U-Pb age with a weighted mean Pb-206/U-238 date of 337.13 +/- 0.37 Ma (ID-TIMS, 95% confidence limits, including tracer calibration uncertainty) and U-Pb age homogeneity on the scale used in LA ICP-MS dating. Inhomogeneities in trace element composition due to primary growth zoning prevent its use as a calibration standard for trace element analysis. The content of U varies from 465 ppm in pristine parts of the grains to similar to 3000 ppm in actinide-rich sectors that correspond to pyramidal faces with a high degree of metamictization (present in ca. 30% of the grains). These domains are easily recognized from high intensities on BSE images and should be avoided during the analysis. Hf isotopic composition of the Plesovice zircon (>0.9 wt.% Hf) is homogenous within and between the grains with a mean Hf-176/Hf-177 value of 0.282492 +/- 0.000013 (2SD). The age and Hf isotopic homogeneity of the Plesovice zircon together with its relatively high U and Pb contents make it an ideal calibration and reference material for laser ablation ICP-MS measurements, especially when using low laser energies and/or small diameters of laser beam required for improved spatial resolution.
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| 21. |
- Szatmari, Peter, et al.
(author)
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Mapping autism risk loci using genetic linkage and chromosomal rearrangements.
- 2007
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 39:3, s. 319-328
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Journal article (peer-reviewed)abstract
- Autism spectrum disorders (ASDs) are common, heritable neurodevelopmental conditions. The genetic architecture of ASDs is complex, requiring large samples to overcome heterogeneity. Here we broaden coverage and sample size relative to other studies of ASDs by using Affymetrix 10K SNP arrays and 1,168 families with at least two affected individuals, performing the largest linkage scan to date while also analyzing copy number variation in these families. Linkage and copy number variation analyses implicate chromosome 11p12-p13 and neurexins, respectively, among other candidate loci. Neurexins team with previously implicated neuroligins for glutamatergic synaptogenesis, highlighting glutamate-related genes as promising candidates for contributing to ASDs.
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