| 1. |
- Alzari, Pedro M., et al.
(författare)
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Implementation of semi-automated cloning and prokaryotic expression screening : the impact of SPINE
- 2006
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Ingår i: Acta Crystallographica Section D. - 0907-4449 .- 1399-0047. ; 62, s. 1103-1113
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Tidskriftsartikel (refereegranskat)abstract
- The implementation of high- throughput ( HTP) cloning and expression screening in Escherichia coli by 14 laboratories in the Structural Proteomics In Europe ( SPINE) consortium is described. Cloning efficiencies of greater than 80% have been achieved for the three non- ligation- based cloning techniques used, namely Gateway, ligation- indendent cloning of PCR products ( LIC- PCR) and In- Fusion, with LIC- PCR emerging as the most cost- effective. On average, two constructs have been made for each of the approximately 1700 protein targets selected by SPINE for protein production. Overall, HTP expression screening in E. coli has yielded 32% soluble constructs, with at least one for 70% of the targets. In addition to the implementation of HTP cloning and expression screening, the development of two novel technologies is described, namely library- based screening for soluble constructs and parallel small- scale high- density fermentation.
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| 2. |
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| 3. |
- Lundberg, Jon O., et al.
(författare)
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Nitrate and nitrite in biology, nutrition and therapeutics
- 2009
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Ingår i: Nature Chemical Biology. - : Springer Science and Business Media LLC. - 1552-4450 .- 1552-4469. ; 5:12, s. 865-869
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Tidskriftsartikel (refereegranskat)abstract
- Inorganic nitrate and nitrite from endogenous or dietary sources are metabolized in vivo to nitric oxide (NO) and other bioactive nitrogen oxides. The nitrate-nitrite-NO pathway is emerging as an important mediator of blood flow regulation, cell signaling, energetics and tissue responses to hypoxia. The latest advances in our understanding of the biochemistry, physiology and therapeutics of nitrate, nitrite and NO were discussed during a recent 2-day meeting at the Nobel Forum, Karolinska Institutet in Stockholm.
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| 4. |
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| 5. |
- Sodergren, Erica, et al.
(författare)
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The genome of the sea urchin Strongylocentrotus purpuratus.
- 2006
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 314:5801, s. 941-52
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Tidskriftsartikel (refereegranskat)abstract
- We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
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| 6. |
- Beisner, Beatrix E., et al.
(författare)
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The role of environmental and spatial processes in structuring lake communities from bacteria to fish
- 2006
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Ingår i: Ecology. - 0012-9658 .- 1939-9170. ; 87:12, s. 2985-2991
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Tidskriftsartikel (refereegranskat)abstract
- We assessed the relative roles of local environmental conditions and dispersal on community structure in a landscape of lakes for the major trophic groups. We use taxonomic presence–absence and abundance data for bacteria, phytoplankton, zooplankton, and fish from 18 lakes in southern Quebec, Canada. The question of interest was whether communities composed of organisms with more limited dispersal abilities, because of size and life history (zooplankton and fish) would show a different effect of lake distribution than communities composed of good dispersers (bacteria and phytoplankton). We examine the variation in structure attributable to local environmental (i.e., lake chemical and physical variables) vs. dispersal predictors (i.e., overland and watercourse distances between lakes) using variation partitioning techniques. Overall, we show that less motile species (crustacean zooplankton and fish) are better predicted by spatial factors than by local environmental ones. Furthermore, we show that for zooplankton abundances, both overland and watercourse dispersal pathways are equally strong, though they may select for different components of the community, while for fish, only watercourses are relevant dispersal pathways. These results suggest that crustacean zooplankton and fish are more constrained by dispersal and therefore more likely to operate as a metacommunity than are bacteria and phytoplankton within this studied landscape.
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| 7. |
- Bidartondo, Martin, et al.
(författare)
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Preserving accuracy in GenBank
- 2008
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Ingår i: Science. ; 319:5870
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 8. |
- Borges Vieira, Alex, et al.
(författare)
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Modelo de Comportamento dos Participantes do SopCast
- 2009
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Ingår i: WebMedia 2009. - New York, NY, USA : ACM. - 9781605588803
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Konferensbidrag (refereegranskat)abstract
- Apesar da crescente popularidade das aplica¸c˜oes de transmiss ˜ao de m´ıdia cont´ınua ao vivo em P2P, a compreens˜ao atual de aspectos importantes do comportamento dos participantes, como o intervalo de chegada entre eles e tempo de permanˆencia na rede, ainda ´e limitada. Este trabalho pretende preencher esta lacuna apresentando uma caracteriza ¸c˜ao do comportamento dos participantes no SopCast, uma das aplica¸c˜oes mais populares de transmiss˜ao ao vivo sobre P2P. A an´alise apresentada inclui propriedades relativas `a sess˜ao, tais como intervalos entre chegada de novos participantes, tempo de permanˆencia, n´umero de sess˜oes q e tempo de inatividade entre sess˜oes. Tamb´em s˜ao apresentadas propriedades das parcerias entre os participantes, como n´umero de parceiros e suas dura¸c˜oes. Al´em disso, o estudo apresentado compreende diferentes canais do Sop- Cast, destacando diferen¸cas nos padr˜oes de comportamento dependendo do conte´udo. As caracteriza¸c˜oes apresentadas definem um modelo dos participantes, que pode ser usado como base para cria¸c˜ao de novos protocolos e gera¸c˜ao de cargas sint´eticas realistas para transmiss˜ao ao vivo em P2P.
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| 9. |
- Cava, Felipe, et al.
(författare)
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Expression and use of superfolder green fluorescent protein at high temperatures in vivo : a tool to study extreme thermophile biology
- 2008
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 10:3, s. 605-613
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Tidskriftsartikel (refereegranskat)abstract
- Superfolder GFP (sGFP) is a variant of the Green Fluorescent Protein that folds efficiently when fused to poorly folded proteins. In this study, we show that sGFP, but not enhanced GFP, is functional in vivo at 70 degrees C in the extreme thermophile Thermus thermophilus (Tth); thus, permitting the use of sGFP as a localization tag in vivo. We created a suite of plasmids that allow the expression of carboxy-terminal sGFP fusion proteins in both Escherichia coli and Tth. In order to demonstrate the facility of sGFP as an in vivo localization tag in Tth, we tagged GroES (the small subunit of the bacterial GroES/GroEL chaperone), NarC (a membrane component of the nitrate respiration apparatus) and PhoA (a TAT-secreted periplasmic protein), and visualized the distribution of the sGFP fusion proteins using confocal microscopy. Fusions to NarC and PhoA produced enzymatically active proteins that complemented both the narC and the phoA strains respectively. Observation of the distribution of the GroES-sGFP protein by confocal microscopy revealed a homogeneous fluorescence in the cells, which is in full agreement with the cytoplasmic nature of GroES, whereas the NarC-sGFP protein was localized to the membrane. Finally, a combination of confocal microscopy and biochemistry revealed that PhoA is localized in the periplasm. We suggest that sGFP will be broadly applicable in characterizing various extreme thermophile systems.
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| 10. |
- Goncalves, Isabel, et al.
(författare)
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Elastin- and Collagen-Rich Human Carotid Plaques Have Increased Levels of the Cysteine Protease Inhibitor Cystatin C.
- 2008
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Ingår i: Journal of Vascular Research. - : S. Karger AG. - 1423-0135 .- 1018-1172. ; 45:5, s. 395-401
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Tidskriftsartikel (refereegranskat)abstract
- Background: Cystatin C is a major inhibitor of the elastin- and collagen-degrading cysteine proteases and may therefore have an important role in preserving atherosclerotic plaque stability. In this study we analyzed the associations between human carotid plaque cystatin C expression and the plaque content of collagen and elastin. Methods: Thirty-one plaques were removed by endarterectomy and homogenized. Cystatin C levels were analyzed by densitometry of Western blots and elastin and collagen levels were determined colorimetrically. Results: The plaque content of cystatin C correlated with total elastin (r = 0.58, p = 0.001) and collagen (r = 0.50, p = 0.004), as well as with cross-linked forms of elastin (r = 0.42, p = 0.022) and collagen (r = 0.52, p = 0.003). Immunohistochemical analysis demonstrated that cystatin C colocalized with elastin and collagen. No correlation was seen between cystatin C and the amount of degraded elastin or collagen in plaques. Conclusion: The positive correlation between cystatin C levels and collagen and elastin levels in plaques supports the notion that cystatin C plays an important role in maintaining atherosclerotic plaque stability. Copyright (c) 2008 S. Karger AG, Basel.
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