| 1. |
- Richards, Stephen, et al.
(author)
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Genome Sequence of the Pea Aphid Acyrthosiphon pisum
- 2010
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In: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 8:2, s. e1000313-
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Journal article (peer-reviewed)abstract
- Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
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| 2. |
- Brownstein, Catherine A., et al.
(author)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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In: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Journal article (peer-reviewed)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 3. |
- Price, Douglas T., et al.
(author)
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Isotopic investigation of human provenience at the eleventh century cemetery of Ndr. Grødbygård, Bornholm, Denmark
- 2013
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In: Danish Journal of Archaeology. - : Det Kgl. Bibliotek/Royal Danish Library. - 2166-2282 .- 2166-2290. ; 1:2, s. 93-112
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Journal article (peer-reviewed)abstract
- Bornholm is a Danish island almost in the center of the southern Baltic Sea. The strategic location of the island, its rich archeology, and its complex geology make it an intriguing location for the isotopic study of past human mobility. The focus of this study is on the large cemetery of Ndr. Grødbygård in the southern part of the island, which dates to the eleventh century AD and contains 553 individuals in 516 graves. The majority of the burials were in a supine position oriented west– east, with the heads to the west, following the tradition of that time. In contrast to the Christian traditions, however, the graves at Grødbygård were richly equipped by Scandinavian standards and some of the burial practices more closely resembled those from the Western Slavic region of the south (present day northeastern Germany and Poland). We have used isotopic analyses to examine the external relations and potential places of origin of the inhabitants of the cemetery. Strontium and oxygen isotope ratios in human tooth enamel provide a signature of place of origin and can be compared to the ratios of the place of burial to determine local or non-local origins. In the case of Bornholm, the local geology is quite complex, with a variety of rocks of different age and composition, resulting in a wide range of strontium isotope sources on the island, complicating the issue of identifying migrants. At the same time, Grødbygård provides an important example of the application of such methods in less than ideal conditions.
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