| 1. |
- Clark, Andrew G., et al.
(författare)
-
Evolution of genes and genomes on the Drosophila phylogeny
- 2007
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 2. |
- Elsik, Christine G., et al.
(författare)
-
The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 3. |
|
|
| 4. |
- Lindblad-Toh, Kerstin, et al.
(författare)
-
Genome sequence, comparative analysis and haplotype structure of the domestic dog.
- 2005
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 438:7069, s. 803-19
-
Tidskriftsartikel (refereegranskat)abstract
- Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
|
|
| 5. |
- Liti, Gianni, et al.
(författare)
-
Population genomics of domestic and wild yeasts.
- 2009
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 458:7236, s. 337-41
-
Tidskriftsartikel (refereegranskat)abstract
- Since the completion of the genome sequence of Saccharomyces cerevisiae in 1996 (refs 1, 2), there has been a large increase in complete genome sequences, accompanied by great advances in our understanding of genome evolution. Although little is known about the natural and life histories of yeasts in the wild, there are an increasing number of studies looking at ecological and geographic distributions, population structure and sexual versus asexual reproduction. Less well understood at the whole genome level are the evolutionary processes acting within populations and species that lead to adaptation to different environments, phenotypic differences and reproductive isolation. Here we present one- to fourfold or more coverage of the genome sequences of over seventy isolates of the baker's yeast S. cerevisiae and its closest relative, Saccharomyces paradoxus. We examine variation in gene content, single nucleotide polymorphisms, nucleotide insertions and deletions, copy numbers and transposable elements. We find that phenotypic variation broadly correlates with global genome-wide phylogenetic relationships. S. paradoxus populations are well delineated along geographic boundaries, whereas the variation among worldwide S. cerevisiae isolates shows less differentiation and is comparable to a single S. paradoxus population. Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of S. cerevisiae consists of a few well-defined, geographically isolated lineages and many different mosaics of these lineages, supporting the idea that human influence provided the opportunity for cross-breeding and production of new combinations of pre-existing variations.
|
|
| 6. |
- Nguyen, Hao G., et al.
(författare)
-
Conditional overexpression of transgenes in megakaryocytes and platelets in vivo
- 2005
-
Ingår i: Blood. - : American Society of Hematology. - 0006-4971 .- 1528-0020. ; 106:5, s. 1559-1564
-
Tidskriftsartikel (refereegranskat)abstract
- Megakaryocyte (MK)-specific transgene expression has proved valuable in studying thrombotic and hemostatic processes. Constitutive expression of genes, however, could result in altered phenotypes due to compensatory mechanisms or lethality. To circumvent these limitations, we used the tetracycline/doxycycline (Tet)-off system to conditionally over-express genes in megakaryocytes and platelets in vivo. We generated 3 transactivator transgenic lines expressing the Tet transactivator element (tTA), under the control of the MK-specific platelet factor 4 promoter (PF4-tTA-VP16). Responder lines were simultaneously generated, each with a bidirectional minimal cytomegalovirus (CMV)-tTA responsive promoter driving prokaryotic β-galactosidase gene, as a cellular reporter, and a gene of interest (in this case, the mitotic regulator Aurora-B). A transactivator founder line that strongly expressed PF4-driven tTA-viral protein 16 (VP16) was crossbred to a responder line. The homozygous double-transgenic mouse line exhibited doxycycline-dependent transgene overexpression in MKs and platelets. Using this line, platelets were conveniently indicated at sites of induced stress by β-galactosidase staining. In addition, we confirmed our earlier report on effects of constitutive expression of Aurora-B, indicating a tight regulation at protein level and a modest effect on MK ploidy. Hence, we generated a new line, PF4-tTA-VP16, that is available for conditionally overexpressing genes of interest in the MK/platelet lineage in vivo.
|
|
| 7. |
- Rohde, Mitchell M., et al.
(författare)
-
An Interactive, physics-based unmanned ground vehicle simulator leveraging open source gaming technology : Progress in the development and application of the virtual autonomous navigation environment (VANE) desktop
- 2009
-
Ingår i: Unmanned Systems Technology XI. - Bellingham, WA : SPIE - International Society for Optical Engineering. - 9780819475985 ; , s. Article number 73321C-
-
Konferensbidrag (refereegranskat)abstract
- It is widely recognized that simulation is pivotal to vehicle development, whether manned or unmanned. There are few dedicated choices, however, for those wishing to perform realistic, end-to-end simulations of unmanned ground vehicles (UGVs). The Virtual Autonomous Navigation Environment (VANE), under development by US Army Engineer Research and Development Center (ERDC), provides such capabilities but utilizes a High Performance Computing (HPC) Computational Testbed (CTB) and is not intended for on-line, real-time performance. A product of the VANE HPC research is a real-time desktop simulation application under development by the authors that provides a portal into the HPC environment as well as interaction with wider-scope semi-automated force simulations (e.g. OneSAF). This VANE desktop application, dubbed the Autonomous Navigation Virtual Environment Laboratory (ANVEL), enables analysis and testing of autonomous vehicle dynamics and terrain/obstacle interaction in real-time with the capability to interact within the HPC constructive geo-environmental CTB for high fidelity sensor evaluations. ANVEL leverages rigorous physics-based vehicle and vehicle-terrain interaction models in conjunction with high-quality, multimedia visualization techniques to form an intuitive, accurate engineering tool. The system provides an adaptable and customizable simulation platform that allows developers a controlled, repeatable testbed for advanced simulations. ANVEL leverages several key technologies not common to traditional engineering simulators, including techniques from the commercial video-game industry. These enable ANVEL to run on inexpensive commercial, off-the-shelf (COTS) hardware. In this paper, the authors d escribe key aspects of ANVEL and its development, as well as several initial applications of the system. © 2009 SPIE.
|
|
| 8. |
|
|
| 9. |
|
|
| 10. |
- Rose, Jeremy, et al.
(författare)
-
The Problem of Agency Re-visited
- 2005
-
Ingår i: Scandinavian Journal of Information Systems. - : Association for Information Systems. - 0905-0167 .- 1901-0990. ; 17:1, s. 187-196
-
Tidskriftsartikel (refereegranskat)
|
|
