| 1. |
- Abdoullaye, Doukary, et al.
(author)
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Permanent genetic resources added to molecular ecology resources database 1 August 2009 - 30 September 2009
- 2010
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In: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:1, s. 232-236
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Journal article (peer-reviewed)abstract
- This article documents the addition of 238 microsatellite marker loci and 72 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Adelges tsugae, Artemisia tridentata, Astroides calycularis, Azorella selago, Botryllus schlosseri, Botrylloides violaceus, Cardiocrinum cordatum var. glehnii, Campylopterus curvipennis, Colocasia esculenta, Cynomys ludovicianus, Cynomys leucurus, Cynomys gunnisoni, Epinephelus coioides, Eunicella singularis, Gammarus pulex, Homoeosoma nebulella, Hyla squirella, Lateolabrax japonicus, Mastomys erythroleucus, Pararge aegeria, Pardosa sierra, Phoenicopterus ruber ruber and Silene latifolia. These loci were cross-tested on the following species: Adelges abietis, Adelges cooleyi, Adelges piceae, Pineus pini, Pineus strobi, Tubastrea micrantha, three other Tubastrea species, Botrylloides fuscus, Botrylloides simodensis, Campylopterus hemileucurus, Campylopterus rufus, Campylopterus largipennis, Campylopterus villaviscensio, Phaethornis longuemareus, Florisuga mellivora, Lampornis amethystinus, Amazilia cyanocephala, Archilochus colubris, Epinephelus lanceolatus, Epinephelus fuscoguttatus, Symbiodinium temperate-A clade, Gammarus fossarum, Gammarus roeselii, Dikerogammarus villosus and Limnomysis benedeni. This article also documents the addition of 72 sequencing primer pairs and 52 allele specific primers for Neophocaena phocaenoides.
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| 2. |
- Adler, Jan-Olof, et al.
(author)
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The upgraded photon tagging facility at the MAX IV Laboratory
- 2013
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In: Nuclear Instruments & Methods in Physics Research. Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment. - : Elsevier BV. - 0167-5087 .- 0168-9002. ; 715, s. 1-10
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Journal article (peer-reviewed)abstract
- A description is given of the upgraded photon tagging facility at the MAX IV Laboratory. Two magnetic spectrometers are used to momentum analyze post-bremsstrahlung electrons. The tagged photon range extends from 10 to 180 MeV with an energy resolution of about 300 keV. The system has been operated at rates up to 4 x 10(6) photons s(-1) MeV (-1). Different diagnostic tools are described as well as the experimental program.
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| 3. |
- Ajawatanawong, Pravech, et al.
(author)
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SeqFIRE : a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments
- 2012
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In: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 40:W1, s. W340-W347
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Journal article (peer-reviewed)abstract
- Analyses of multiple sequence alignments generally focus on well-defined conserved sequence blocks, while the rest of the alignment is largely ignored or discarded. This is especially true in phylogenomics, where large multigene datasets are produced through automated pipelines. However, some of the most powerful phylogenetic markers have been found in the variable length regions of multiple alignments, particularly insertions/deletions (indels) in protein sequences. We have developed Sequence Feature and Indel Region Extractor (SeqFIRE) to enable the automated identification and extraction of indels from protein sequence alignments. The program can also extract conserved blocks and identify fast evolving sites using a combination of conservation and entropy. All major variables can be adjusted by the user, allowing them to identify the sets of variables most suited to a particular analysis or dataset. Thus, all major tasks in preparing an alignment for further analysis are combined in a single flexible and user-friendly program. The output includes a numbered list of indels, alignments in NEXUS format with indels annotated or removed and indel-only matrices. SeqFIRE is a user-friendly web application, freely available online at www.seqfire.org/.
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| 4. |
- Almeida, Rafael M., et al.
(author)
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Correspondence : Emissions from Amazonian dams
- 2013
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In: Nature Climate Change. - : Springer Science and Business Media LLC. - 1758-678X .- 1758-6798. ; 3:12, s. 1005-1005
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Journal article (other academic/artistic)
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| 5. |
- Asselbergs, Folkert W., et al.
(author)
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Large-Scale Gene-Centric Meta-analysis across 32 Studies Identifies Multiple Lipid Loci
- 2012
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In: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297. ; 91:5, s. 823-838
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Journal article (peer-reviewed)abstract
- Genome-wide association studies (GWASs) have identified many SNPs underlying variations in plasma-lipid levels. We explore whether additional loci associated with plasma-lipid phenotypes, such as high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), total cholesterol (TC), and triglycerides (TGs), can be identified by a dense gene-centric approach. Our meta-analysis of 32 studies in 66,240 individuals of European ancestry was based on the custom similar to 50,000 SNP genotyping array (the ITMAT-Broad-CARe array) covering similar to 2,000 candidate genes. SNP-lipid associations were replicated either in a cohort comprising an additional 24,736 samples or within the Global Lipid Genetic Consortium. We identified four, six, ten, and four unreported SNPs in established lipid genes for HDL-C, LDL-C, TC, and TGs, respectively. We also identified several lipid-related SNPs in previously unreported genes: DGAT2, HCAR2, GPIHBP1, PPARG, and FTO for HDL-C; SOCS3, APOH, SPTY2D1, BRCA2, and VLDLR for LDL-C; SOCS3, UGT1A1, BRCA2, UBE3B, FCGR2A, CHUK, and INSIG2 for TC; and SERPINF2, C4B, GCK, GATA4, INSR, and LPAL2 for TGs. The proportion of explained phenotypic variance in the subset of studies providing individual-level data was 9.9% for HDL-C, 9.5% for LDL-C, 10.3% for TC, and 8.0% for TGs. This large meta-analysis of lipid phenotypes with the use of a dense gene-centric approach identified multiple SNPs not previously described in established lipid genes and several previously unknown loci. The explained phenotypic variance from this approach was comparable to that from a meta-analysis of GWAS data, suggesting that a focused genotyping approach can further increase the understanding of heritability of plasma lipids.
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| 6. |
- Assimes, Themistocles L., et al.
(author)
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Lack of Association Between the Trp719Arg Polymorphism in Kinesin-Like Protein-6 and Coronary Artery Disease in 19 Case-Control Studies
- 2010
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In: Journal of the American College of Cardiology. - : Elsevier BV. - 0735-1097. ; 56:19, s. 1552-1563
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Journal article (peer-reviewed)abstract
- Objectives We sought to replicate the association between the kinesin-like protein 6 (KIF6) Trp719Arg polymorphism (rs20455), and clinical coronary artery disease (CAD). Background Recent prospective studies suggest that carriers of the 719Arg allele in KIF6 are at increased risk of clinical CAD compared with noncarriers. Methods The KIF6 Trp719Arg polymorphism (rs20455) was genotyped in 19 case-control studies of nonfatal CAD either as part of a genome-wide association study or in a formal attempt to replicate the initial positive reports. Results A total of 17,000 cases and 39,369 controls of European descent as well as a modest number of South Asians, African Americans, Hispanics, East Asians, and admixed cases and controls were successfully genotyped. None of the 19 studies demonstrated an increased risk of CAD in carriers of the 719Arg allele compared with noncarriers. Regression analyses and fixed-effects meta-analyses ruled out with high degree of confidence an increase of >= 2% in the risk of CAD among European 719Arg carriers. We also observed no increase in the risk of CAD among 719Arg carriers in the subset of Europeans with early-onset disease (younger than 50 years of age for men and younger than 60 years of age for women) compared with similarly aged controls as well as all non-European subgroups. Conclusions The KIF6 Trp719Arg polymorphism was not associated with the risk of clinical CAD in this large replication study. (J Am Coll Cardiol 2010;56:1552-63) (C) 2010 by the American College of Cardiology Foundation
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| 7. |
- Barros, Nathan, et al.
(author)
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Carbon emission from hydroelectric reservoirs linked to reservoir age and latitude
- 2011
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In: Nature Geoscience. - : Nature Publishing Group. - 1752-0894 .- 1752-0908. ; 4:9, s. 593-596
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Journal article (peer-reviewed)abstract
- Hydroelectric reservoirs cover an area of 3.4 x 10(5) km(2) and comprise about 20% of all reservoirs. In addition, they contain large stores of formerly terrestrial organic carbon. Significant amounts of greenhouse gases are emitted(2), especially in the early years following reservoir creation, but the global extent of these emissions is poorly known. Previous estimates of emissions from all types of reservoir indicate that these human-made systems emit 321 Tg of carbon per year (ref. 4). Here we assess the emissions of carbon dioxide and methane from hydroelectric reservoirs, on the basis of data from 85 globally distributed hydroelectric reservoirs that account for 20% of the global area of these systems. We relate the emissions to reservoir age, location biome, morphometric features and chemical status. We estimate that hydroelectric reservoirs emit about 48 Tg C as CO(2) and 3 Tg C as CH(4), corresponding to 4% of global carbon emissions from inland waters. Our estimates are smaller than previous estimates on the basis of more limited data. Carbon emissions are correlated to reservoir age and latitude, with the highest emission rates from the tropical Amazon region. We conclude that future emissions will be highly dependent on the geographic location of new hydroelectric reservoirs.
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| 8. |
- Bassett, Andrew R., et al.
(author)
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Understanding functional miRNA-target interactions in vivo by site-specific genome engineering
- 2014
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 5, s. 4640-
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Journal article (peer-reviewed)abstract
- MicroRNA (miRNA) target recognition is largely dictated by short 'seed' sequences, and single miRNAs therefore have the potential to regulate a large number of genes. Understanding the contribution of specific miRNA-target interactions to the regulation of biological processes in vivo remains challenging. Here we use transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 technologies to interrogate the functional relevance of predicted miRNA response elements (MREs) to post-transcriptional silencing in zebrafish and Drosophila. We also demonstrate an effective strategy that uses CRISPR-mediated homology-directed repair with short oligonucleotide donors for the assessment of MRE activity in human cells. These methods facilitate analysis of the direct phenotypic consequences resulting from blocking specific miRNA-MRE interactions at any point during development.
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| 9. |
- Behnam, Moris, et al.
(author)
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On Optimal Real-time Subsystem-Interface Generation in the Presence of Shared Resources
- 2010
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In: Proceedings of the 15th IEEE International Conference on Emerging Technologies and Factory Automation, ETFA 2010. - Bilbao, Spain. - 9781424468508
-
Conference paper (peer-reviewed)abstract
- The Hierarchical Scheduling Framework (HSF) has been introduced as a design-time framework enabling compositional schedulability analysis of embedded software systems with real-time properties. However, supporting resource sharing in HSF is a major challenge, since it increases the amount of CPU resources required to guarantee schedulability of the hard real time tasks, and it decreases the composability at the system level. In this paper, we focus on a compositional framework called the bounded-delay resource open environment (BROE) server, and we identify key parameters of this framework that have a great effect on how the framework will utilize CPU resources. In addition, we show how to select optimal values for these parameters in order to reduce the required CPU resource
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| 10. |
- Bennett, Nathan J., et al.
(author)
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The capacity to adapt?: Communities in a changing climate, environment, and economy on the northern Andaman coast of Thailand
- 2014
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In: Ecology and Society. - 1708-3087 .- 1708-3087. ; 19
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Journal article (peer-reviewed)abstract
- The health and productivity of marine ecosystems, habitats, and fisheries are deteriorating on the Andaman coast of Thailand. Because of their high dependence on natural resources and proximity to the ocean, coastal communities are particularly vulnerable to climate-induced changes in the marine environment. These communities must also adapt to the impacts of management interventions and conservation initiatives, including marine protected areas, which have livelihood implications. Further, communities on the Andaman coast are also experiencing a range of new economic opportunities associated in particular with tourism and agriculture. These complex and ongoing changes require integrated assessment of, and deliberate planning to increase, the adaptive capacity of communities so that they may respond to: (1) environmental degradation and fisheries declines through effective management interventions or conservation initiatives, (2) new economic opportunities to reduce dependence on fisheries, and (3) the increasing impacts of climate change. Our results are from a mixed methods study, which used surveys and interviews to examine multiple dimensions of the adaptive capacity of seven island communities near marine protected areas on the Andaman coast of Thailand. Results show that communities had low adaptive capacity with respect to environmental degradation and fisheries declines, and to management and conservation interventions, as well as uneven levels of adaptive capacity to economic opportunities. Though communities and households were experiencing the impacts of climate change, especially storm events, changing seasons and weather patterns, and erosion, they were reacting to these changes with limited knowledge of climate change per se. We recommend interventions, in the form of policies, programs, and actions, at multiple scales for increasing the adaptive capacity of Thailand's coastal communities to change. The analytical and methodological approach used for examining adaptive capacity could be easily modified and applied to other contexts and locales. © 2014 by the author(s).
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