| 1. |
- 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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| 2. |
- 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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| 3. |
- 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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| 4. |
- Darakchieva, V., et al.
(author)
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Phonons in strained AlGaN/GaN superlattices
- 2007
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In: Physica Status Solidi. C, Current topics in solid state physics. - : Wiley. - 1610-1634 .- 1610-1642. ; 4:1, s. 170-174
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Journal article (peer-reviewed)abstract
- Phonons in strained AlGaN/GaN superlattices (SLs) with constant periods but different Al composition have been studied using a combination of infrared spectroscopic ellipsometry and Raman scattering spectroscopy. The following SL modes were identified: i) AlGaN localized E1(TO) modes identified for the first time and AlGaN localized A1 (LO) phonons; ii) GaN localized E2, E1(TO) and A1(LO) phonons; iii) delocalized E1(LO) phonons; iv) A1(TO) phonon; v) two modes around 660 cm-1 and 594-625 cm-1, respectively, not predicted by theory. The effects of strain and composition on the phonon frequencies were established and discussed.
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| 5. |
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| 6. |
- 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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| 7. |
- Paskova, T., et al.
(author)
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Strain-free low-defect-density bulk GaN with nonpolar orientations
- 2006
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In: MRS Proceedings. - : Springer Science and Business Media LLC. - 1946-4274.
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Conference paper (peer-reviewed)abstract
- Bulk GaN sliced in bars along (11-20) and (1-100) planes from a boule grown in the [0001] direction by HVPE was confirmed as strain free material with a low dislocation density by using several characterization techniques. The high-structural quality of the material allows photoluminescence studies of free excitons, principal donor bound excitons and their twoelectron satellites with regard to the optical selection rules. Raman scattering study of the bulk GaN with nonpolar orientations allows a direct access to the active phonon modes and a direct determination of their strain-free positions.
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| 8. |
- Rahmathullah, Abu Sajana, 1986, et al.
(author)
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A low-complexity algorithm for intrusion detection in a PIR-based Wireless Sensor Network
- 2009
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In: Intelligent Sensors, Sensor Networks and Information Processing (ISSNIP), 2009, Melbourne, Australia. - 9781424435173 ; , s. 337 - 342
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Conference paper (peer-reviewed)abstract
- We present a low-complexity algorithm for intrusion detection in the presence of clutter arising from wind-blown vegetation, using passive infra-red (PIR) sensors in a wireless sensor network (WSN). The algorithm is based on a combination of Haar transform (HT) and support-vector-machine (SVM) based training and was field tested in a network setting comprising of 15-20 sensing nodes. Also contained in this paper is a closed-form expression for the signal generated by an intruder moving at a constant velocity. It is shown how this expression can be exploited to determine the direction of motion information and the velocity of the intruder from the signals of three well-positioned sensors.
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| 9. |
- Treebak, Jonas T, et al.
(author)
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AMPK-mediated AS160 phosphorylation in skeletal muscle is dependent on AMPK catalytic and regulatory subunits.
- 2006
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In: Diabetes. - : American Diabetes Association. - 0012-1797 .- 1939-327X. ; 55:7, s. 2051-2058
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Journal article (peer-reviewed)abstract
- AMP-activated protein kinase (AMPK) is a heterotrimeric protein that regulates glucose transport mediated by cellular stress or pharmacological agonists such as 5-aminoimidazole-4-carboxamide 1 beta-D-ribonucleoside (AICAR). AS160, a Rab GTPase-activating protein, provides a mechanism linking AMPK signaling to glucose uptake. We show that AICAR increases AMPK, acetyl-CoA carboxylase, and AS160 phosphorylation by insulin-independent mechanisms in isolated skeletal muscle. Recombinant AMPK heterotrimeric complexes (alpha 1 beta 1 gamma l and alpha 2 beta 2 gamma 1) phosphorylate AS160 in a cell-free assay. In mice deficient in AMPK signaling (alpha 2 AMPK knockout [KO], alpha 2 AMPK kinase dead [KD], and gamma 3 AMPK KO), AICAR effects on AS160 phosphorylation were severely blunted, highlighting that complexes containing alpha 2 and gamma 3 are necessary for AICAR-stimulated AS160 phosphorylation in intact skeletal muscle. Contraction-mediated AS160 phosphorylation was also impaired in alpha 2 AMPK KO and KD but not gamma 3 AMPK KO mice. Our results implicate AS160 as a downstream target of AMPK.
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| 10. |
- 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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