| 1. |
- Clark, Andrew G., et al.
(author)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Journal article (peer-reviewed)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 2. |
- Sodergren, Erica, et al.
(author)
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The genome of the sea urchin Strongylocentrotus purpuratus.
- 2006
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In: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 314:5801, s. 941-52
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Journal article (peer-reviewed)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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| 3. |
- Tranvik, Lars J., et al.
(author)
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Lakes and reservoirs as regulators of carbon cycling and climate
- 2009
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In: Limnology and Oceanography. - : Wiley. - 0024-3590 .- 1939-5590. ; 54:6:2, s. 2298-2314
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Research review (peer-reviewed)abstract
- We explore the role of lakes in carbon cycling and global climate, examine the mechanisms influencing carbon pools and transformations in lakes, and discuss how the metabolism of carbon in the inland waters is likely to change in response to climate. Furthermore, we project changes as global climate change in the abundance and spatial distribution of lakes in the biosphere, and we revise the estimate for the global extent of carbon transformation in inland waters. This synthesis demonstrates that the global annual emissions of carbon dioxide from inland waters to the atmosphere are similar in magnitude to the carbon dioxide uptake by the oceans and that the global burial of organic carbon in inland water sediments exceeds organic carbon sequestration on the ocean floor. The role of inland waters in global carbon cycling and climate forcing may be changed by human activities, including construction of impoundments, which accumulate large amounts of carbon in sediments and emit large amounts of methane to the atmosphere. Methane emissions are also expected from lakes on melting permafrost. The synthesis presented here indicates that (1) inland waters constitute a significant component of the global carbon cycle, (2) their contribution to this cycle has significantly changed as a result of human activities, and (3) they will continue to change in response to future climate change causing decreased as well as increased abundance of lakes as well as increases in the number of aquatic impoundments.
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| 4. |
- Yoo, S. J. B., et al.
(author)
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Spectral phase encoded time spread optical code division multiple access technology for next generation communication networks Invited
- 2007
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In: Journal of Optical Networking. - 1536-5379. ; 6:10, s. 1210-1227
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Journal article (peer-reviewed)abstract
- We overview and summarize the progress of the spectral phase encoded time spreading (SPECTS) optical code division multiple access (O-CDMA) technology. Recent progress included a demonstration of a 320 Gbit/s (32-user x 10 Gbit/s) all-optical passive optical network testbed based on the SPECTS O-CDMA technology and a theoretical prediction of the spectral efficiency at 100% and above. In particular, InP-based integrated photonics allows implementation of SPECTS O-CDMA transmitters and receivers monolithically integrated on a chip. The integrated InP chip technology not only allows robust and compact configurations for practical and low-cost O-CDMA network deployments but also offers code reconfigurations at rapid rates for secure communication applications.
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| 5. |
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| 6. |
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| 7. |
- Haas, Brian J., et al.
(author)
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Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans
- 2009
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 461:7262, s. 393-398
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Journal article (peer-reviewed)abstract
- Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement(1). To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population(1). Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion(2). Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars(3,4). Here we report the sequence of the P. infestans genome, which at similar to 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for similar to 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.
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| 8. |
- Olsson, Fredrik, et al.
(author)
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Epitaxial lateral overgrowth of InP in micro line and submicro mesh openings
- 2007
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In: 2007 International Conference on Indium Phosphide and Related Materials. ; , s. 311-314
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Conference paper (peer-reviewed)abstract
- Towards achieving a large area of InP on silicon, a study of ELOG of InP on InP has been undertaken on lines with different orientations and with openings that are 100 mu m long and 10 gm wide. This knowledge has been transposed on sub-micro mesh structures. By this method we have obtained 2 gm thick InP on a mesh patterned InP. The layer exhibits room temperature photoluminescence (PL) with a full width half maximum of 24 nm. We propose that this intensity can be increased if nano-sized openings are used.
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| 9. |
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| 10. |
- Andersson, Arne, et al.
(author)
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Amyloid Deposition in Transplanted Human Pancreatic Islets : A Conceivable Cause of Their Long-Term Failure
- 2008
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In: EXPERIMENTAL DIABETES RESEARCH. - : Hindawi Limited. - 1687-5214 .- 1687-5303. ; 2008:562985
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Journal article (peer-reviewed)abstract
- Following the encouraging report of the Edmonton group, there was a rejuvenation of the islet transplantation field. After that, more pessimistic views spread when long-term results of the clinical outcome were published. A progressive loss of the beta-cell function meant that almost all patients were back on insulin therapy after 5 years. More than 10 years ago, we demonstrated that amyloid deposits rapidly formed in human islets and in mouse islets transgenic for human IAPP when grafted into nude mice. It is, therefore, conceivable to consider amyloid formation as one potential candidate for the long-term failure. The present paper reviews attempts in our laboratories to elucidate the dynamics of and mechanisms behind the formation of amyloid in transplanted islets with special emphasis on the impact of long-term hyperglycemia.
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| 11. |
- Azarov, A.Yu., et al.
(author)
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High dose Fe implantation of gan : Damage build-up and dopant redistribution
- 2008
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In: PROCEEDINGS OF THE 17TH INTERNATIONAL VACUUM CONGRESS/13TH INTERNATIONAL CONFERENCE ON SURFACE SCIENCE/INTERNATIONAL CONFERENCE ON NANOSCIENCE AND TECHNOLOGY. - : IOP Publishing. ; 100:4, s. 042036-
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Conference paper (peer-reviewed)abstract
- Undoped GaN epilayers implanted at room temperature with 50-325 keV Fe + ions in the fluence range of 1015 - 1017 ions/cm are studied by a combination of Rutherford backscattering/channeling spectrometry and time-of-flight elastic recoil detection analysis. Results show that for high ion fluences (>1 × 1016 cm-2) enhanced Fe concentration closer to the surface is observed. The Fe redistribution towards the surface increases as the ion fluence increases. Our findings are attributed to radiation enhanced diffusion during ion implantation and increasing of Fe diffusivity in the implantation-induced amorphous phase near the surface.
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| 12. |
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| 13. |
- Cao, J., et al.
(author)
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Error-free spectral encoding and decoding operation of InP O-CDMA encoder
- 2006
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In: 2006 Optical Fiber Communication Conference, and the 2006 National Fiber Optic Engineers Conference. - : IEEE. - 1557528039 - 9781557528032
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Conference paper (peer-reviewed)abstract
- We report error-free spectral encoding and decoding operation of an InP monolithic, ultra-compact optical-CDMA encoder/decoder photonic chip pair. The experimental results demonstrate the strong potential for realizing high performance O-CDMA networks with InP micro-systems.
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| 14. |
- Chaloupka, Milani, et al.
(author)
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Encouraging outlook for recovery of a once severely exploited marine megaherbivore
- 2008
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In: Global Ecology and Biogeography. - : Wiley. - 1466-8238 .- 1466-822X. ; 17:2, s. 297-304
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Journal article (peer-reviewed)abstract
- Aim To critically review the status of the green sea turtle (Chelonia mydas) using the best available scientific studies as there is a prevailing view that this species is globally endangered and its marine ecosystem functions compromised. Location Ogasawara (Japan), Hawaii (USA), Great Barrier Reef (Australia), Florida (USA), Tortuguero (Costa Rica). Methods We compiled seasonal nesting activity data from all reliable continuous long-term studies (> 25 years), which comprised data series for six of the world's major green turtle rookeries. We estimated the underlying time-specific trend in these six rookery-specific nester or nest abundance series using a generalized smoothing spline regression approach. Results Estimated rates of nesting population increase ranged from c. 4-14% per annum over the past two to three decades. These rates varied considerably among the rookeries, reflecting the level of historical exploitation. Similar increases in nesting population were also evident for many other green turtle stocks that have been monitored for shorter durations than the long-term studies presented here. Main conclusions We show that six of the major green turtle nesting populations in the world have been increasing over the past two to three decades following protection from human hazards such as exploitation of eggs and turtles. This population recovery or rebound capacity is encouraging and suggests that the green turtle is not on the brink of global extinction even though some stocks have been seriously depleted and are still below historical abundance levels. This demonstrates that relatively simple conservation strategies can have a profound effect on the recovery of once-depleted green turtle stocks and presumably the restoration of their ecological function as major marine consumers.
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| 15. |
- Cordain, L, et al.
(author)
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Origins and evolution of the Western diet: health implications for the 21st century
- 2005
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In: American Journal of Clinical Nutrition. - 1938-3207. ; 81:2, s. 341-354
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Journal article (other academic/artistic)abstract
- There is growing awareness that the profound changes in the environment (eg, in diet and other lifestyle conditions) that began with the introduction of agriculture and animal husbandry approximate to10 000 y ago occurred too recently on an evolutionary time scale for the human genome to adjust. In conjunction with this discordance between our ancient, genetically determined biology and the nutritional, cultural, and activity patterns of contemporary Western populations, many of the so-called diseases of civilization have emerged. In particular, food staples and food-processing procedures introduced during the Neolithic and Industrial Periods have fundamentally altered 7 crucial nutritional characteristics of ancestral hominin diets: 1) glycemic load, 2) fatty acid composition, 3) macronutrient composition, 4) micronutrient density, 5) acid-base balance, 6) sodium-potassium ratio, and 7) fiber content. The evolutionary collision of our ancient genome with the nutritional qualities of recently introduced foods may underlie many of the chronic diseases of Western civilization.
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| 16. |
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| 17. |
- da Silva Xavier, Gabriela, et al.
(author)
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TCF7L2 regulates late events in insulin secretion from pancreatic islet beta-cells
- 2009
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In: Diabetes. - : American Diabetes Association. - 0012-1797 .- 1939-327X. ; 58:4, s. 894-905
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Journal article (peer-reviewed)abstract
- OBJECTIVE: Polymorphisms in the human TCF7L2 gene are associated with reduced insulin secretion and an increased risk of type 2 diabetes. However, the mechanisms by which TCF7L2 affect insulin secretion are still unclear. We define the effects of TCF7L2 expression level on mature beta-cell function and suggest a potential mechanism for its actions. RESEARCH DESIGN AND METHODS: TCF7L2 expression in rodent islets and beta-cell lines was altered using RNAi or adenoviral transduction. Beta-cell gene profiles were measured by quantitative real-time PCR and the effects on intracellular signaling and exocytosis by live cell imaging, electron microscopy, and patch clamp electrophysiology. RESULTS: Reducing TCF7L2 expression levels by RNAi decreased glucose- but not KCl-induced insulin secretion. The glucose-induced increments in both ATP/ADP ratio and cytosolic free Ca2+ concentration ([Ca2+]i) were increased compared with controls. Overexpression of TCF7L2 exerted minor inhibitory effects on glucose-regulated changes in [Ca2+]i and insulin release. Gene expression profiling in TCF7L2-silenced cells revealed increased levels of mRNA encoding syntaxin 1A but decreased Munc18–1 and ZnT8 mRNA. Whereas the number of morphologically docked vesicles was unchanged by TCF7L2 suppression, secretory granule movement increased and capacitance changes decreased, indicative of defective vesicle fusion. CONCLUSION: TCF7L2 is involved in maintaining expression of beta-cell genes regulating secretory granule fusion. Defective insulin exocytosis may thus underlie increased diabetes incidence in carriers of the at-risk TCF7L2 alleles.
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| 18. |
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| 19. |
- Fox, A, et al.
(author)
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Large particles are responsible for elevated bacterial marker levels in school air upon occupation
- 2005
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In: Journal of Environmental Monitoring. - : Royal Society of Chemistry (RSC). - 1464-0325 .- 1464-0333. ; 7:5, s. 450-456
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Journal article (peer-reviewed)abstract
- Muramic acid (Mur) is found in bacterial peptidoglycan ( PG) whereas 3-hydroxy fatty acids (3-OH FAs) are found in Gram-negative bacterial lipopolysaccharide (LPS). Thus Mur and 3-OH FAs serve as markers to assess bacterial levels in indoor air. An initial survey, in a school, demonstrated that the levels of dust, PG and LPS (pmol m(-3)) were each much higher in occupied rooms than in the same rooms when unoccupied. In each instance, the Mur content of dust was increased and the hydroxy fatty acid distribution changed similarly suggesting an alteration in the bacterial population. Here, findings are compared with results from two additional schools. Follow-up aerosol monitoring by particle size was also performed for the first time for all 3 schools. The particle size distribution was shown to be quite different in occupied versus unoccupied schoolrooms. Within individual classrooms, concentrations of airborne particles ≥ 0.8 μ m in diameter, and CO2 were correlated. This suggests that the increased levels of larger particles are responsible for elevation of bacterial markers during occupation. Release of culturable and non-culturable bacteria or bacterial aggregates from children (e.g. from flaking skin) might explain this phenomenon.
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| 20. |
- Hansson, Sebastian, et al.
(author)
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Crystal structure of a mutant elongation factor G trapped with a GTP analogue
- 2005
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In: FEBS Letters. - : Wiley. - 1873-3468 .- 0014-5793. ; 579:20, s. 4492-4497
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Journal article (peer-reviewed)abstract
- Elongation factor G (EF-G) is a G protein factor that catalyzes the translocation step in protein synthesis on the ribosome. Its GTP conformation in the absence of the ribosome is currently unknown. We present the structure of a mutant EF-G (T84A) in complex with the non-hydrolysable GTP analogue GDPNP. The crystal structure provides a first insight into conformational changes induced in EF-G by GTP. Comparison of this structure with that of EF-G in complex with GDP suggests that the GTP and GDP conformations in solution are very similar and that the major contribution to the active GTPase conformation, which is quite different, therefore comes from its interaction with the ribosome. (c) 2005 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
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| 21. |
- Holmström, Petter, et al.
(author)
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Intersubband photonic devices by group-III nitrides
- 2007
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In: Optoelectronic Materials And Devices II. - : SPIE. - 9780819469458 ; , s. N7821-N7821
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Conference paper (peer-reviewed)abstract
- The characteristics of intersubband transitions in III-nitride quantum wells are promising for detectors and all-optical switches through a high intrinsic speed (similar to 1 THz), and can also provide a high optical saturation power and a desired small negative chirp parameter in electroabsorption modulators. The high LO-phonon energy allows to improve the operating temperature of THz emitters. Recent achievements and prospects for intersubband III-nitride photonic devices, mainly for lambda=1.55 mu m, are briefly reviewed. Further, means to enhance material quality by achieving crack-free growth of GaN/AlN multiple-quantum-well (MQW) structures, and by employing intersubband transitions in multiple-quantum-disk (MQD) structures incorporated into dislocation free GaN nanocolumns are discussed. We investigate the occurrence of cracks in MBE-grown GaN/AlN MQWs on GaN MOVPE templates with respect to the buffer layer, the number of QWs and the temperature reduction rate after growth. Intersubband absorption in GaN/AlN MQDs in the wavelength range 1.38-1.72 mu m is demonstrated in three samples grown on Si(111).
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| 22. |
- Iovan, Adrian, et al.
(author)
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Spin diode based on Fe/MgO double tunnel junction
- 2008
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In: Nano letters (Print). - : American Chemical Society (ACS). - 1530-6984 .- 1530-6992. ; 8:3, s. 805-809
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Journal article (peer-reviewed)abstract
- We demonstrate a spin diode consisting of a semiconductor-free nanoscale Fe/MgO-based double tunnel junction. The device exhibits a near perfect spin-valve effect combined with a strong diode effect. The mechanism consistent with our data is resonant tunneling through discrete states in the middle ferromagnetic layer sandwiched by tunnel barriers of different spin-dependent transparency. The observed magnetoresistance is a record high > 1000%, essentially making the structure an on/off spin switch. This, combined with the strong diode effect, similar to 100, demonstrates a new device principle, promising for memory and reprogrammable logic applications.
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| 23. |
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| 24. |
- Lankinen, A., et al.
(author)
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Crystal Defects and Strain of Epitaxial InP Layers Laterally Overgrown on Si
- 2006
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In: Crystal Growth & Design. - : American Chemical Society (ACS). - 1528-7483 .- 1528-7505. ; 6:5, s. 1096-1100
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Journal article (peer-reviewed)abstract
- Defects in epitaxial laterally overgrown (ELO) InP layers are examined by high-resolution X-ray diffraction and synchrotron X-ray back-reflection and transmission topography. X-ray diffraction maps produce information about the overall crystal quality of the epitaxial layers in the InP ELO sample. The topographs show small angle boundaries, and the associated dislocations are located at the boundaries between the crystallites; allowing for their relative tilt, the maximum value for this is 0.06 degrees. No defects inside the crystallites can be seen in the topographs, except for a small bending of 0.04 degrees at most, of the ELO lattice planes. The section topographs show deformed X-ray interference fringes resulting from the large strain of the silicon lattice below the seeding areas.
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| 25. |
- Lourdudoss, Sebastian, et al.
(author)
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Heteroepitaxy and selective epitaxy for discrete and integrated devices
- 2006
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In: 2006 CONFERENCE ON OPTOELECTRONIC AND MICROELECTRONIC MATERIALS & DEVICES. - NEW YORK : IEEE. - 9781424405770 ; , s. 309-311
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Conference paper (peer-reviewed)abstract
- We present first results on heteroepitaxy of InP on silicon on insulator (SOI). We also demonstrate InP nanopillar fabrication by means of selective epitaxy. Selective epitaxy is also exploited to fabricate advanced photonic integrated devices for Optical Code Division Multiplex Access (OCDMA) networking applications.
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