| 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. |
- Graves, Spencer B., et al.
(author)
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Accelerated testing of on-board diagnostics
- 2007
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In: Quality and Reliability Engineering International. - : Wiley. - 0748-8017 .- 1099-1638. ; 23:2, s. 189-201
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Journal article (peer-reviewed)abstract
- Modern products frequently feature monitors designed to detect actual or impending malfunctions. False alarms (Type I errors) or excessive delays in detecting real malfunctions (Type II errors) can seriously reduce monitor utility. Sound engineering practice includes physical evaluation of error rates. Type II error rates are relatively easy to evaluate empirically. However, adequate evaluation of a low Type I error rate is difficult without using accelerated testing concepts, inducing false alarms using artificially low thresholds and then selecting production thresholds by appropriate extrapolation, as outlined here. This acceleration methodology allows for informed determination of detection thresholds and confidence in monitor performance with substantial reductions over current alternatives in time and cost required for monitor development
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| 3. |
- Hill, Deirdre A., et al.
(author)
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Breast cancer risk following radiotherapy for Hodgkin lymphoma : modification by other risk factors
- 2005
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In: Blood. - : American Society of Hematology. - 0006-4971 .- 1528-0020. ; 106:10, s. 3358-65
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Journal article (peer-reviewed)abstract
- The importance of genetic and other risk factors in the development of breast cancer after radiotherapy (RT) for Hodgkin lymphoma (HL) has not been determined. We analyzed data from a breast cancer case-control study (105 patients, 266 control subjects) conducted among 3 817 survivors of HL diagnosed at age 30 years or younger in 6 population-based cancer registries. Odds ratios (ORs) and excess relative risks (ERRs) were calculated using conditional regression. Women who received RT exposure (> or = 5 Gy radiation dose to the breast) had a 2.7-fold increased breast cancer risk (95% confidence interval (CI) 1.4-5.2), compared with those given less than 5 Gy. RT exposure (> or = 5 Gy) was associated with an OR of 0.8 (95% CI, 0.2-3.4) among women with a first- or second-degree family history of breast or ovarian cancer, and 5.8 (95% CI, 2.1-16.3) among all other women (interaction P = .03). History of a live birth appeared to increase the breast cancer risk associated with RT among women not treated with ovarian-damaging therapies. Breast cancer risk following RT varied little according to other factors. The additional increased relative risk of breast cancer after RT for HL is unlikely to be larger among women with a family history of breast or ovarian cancer than among other women.
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| 4. |
- Miller, Webb, et al.
(author)
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Sequencing the nuclear genome of the extinct woolly mammoth.
- 2008
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 456:7220, s. 387-390
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Journal article (peer-reviewed)abstract
- In 1994, two independent groups extracted DNA from several Pleistocene epoch mammoths and noted differences among individual specimens. Subsequently, DNA sequences have been published for a number of extinct species. However, such ancient DNA is often fragmented and damaged, and studies to date have typically focused on short mitochondrial sequences, never yielding more than a fraction of a per cent of any nuclear genome. Here we describe 4.17 billion bases (Gb) of sequence from several mammoth specimens, 3.3 billion (80%) of which are from the woolly mammoth (Mammuthus primigenius) genome and thus comprise an extensive set of genome-wide sequence from an extinct species. Our data support earlier reports that elephantid genomes exceed 4 Gb. The estimated divergence rate between mammoth and African elephant is half of that between human and chimpanzee. The observed number of nucleotide differences between two particular mammoths was approximately one-eighth of that between one of them and the African elephant, corresponding to a separation between the mammoths of 1.5-2.0 Myr. The estimated probability that orthologous elephant and mammoth amino acids differ is 0.002, corresponding to about one residue per protein. Differences were discovered between mammoth and African elephant in amino-acid positions that are otherwise invariant over several billion years of combined mammalian evolution. This study shows that nuclear genome sequencing of extinct species can reveal population differences not evident from the fossil record, and perhaps even discover genetic factors that affect extinction.
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| 5. |
- Mlynczak, Martin G., et al.
(author)
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Evidence for a solar cycle influence on the infrared energy budget and radiative cooling of the thermosphere
- 2007
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In: Journal of Geophysical Research - Space Physics. - 2169-9380 .- 2169-9402. ; 112:A12
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Journal article (peer-reviewed)abstract
- We present direct observational evidence for solar cycle influence on the infrared energy budget and radiative cooling of the thermosphere. By analyzing nearly five years of data from the Sounding of the Atmosphere using Broadband Emission Radiometry (SABER) instrument, we show that the annual mean infrared power radiated by the nitric oxide (NO) molecule at 5.3 μm has decreased by a factor of 2.9. This decrease is correlated (r = 0.96) with the decrease in the annual mean F10.7 solar index. Despite the sharp decrease in radiated power (which is equivalent to a decrease in the vertical integrated radiative cooling rate), the variability of the power as given in the standard deviation of the annual means remains approximately constant. A simple relationship is shown to exist between the infrared power radiated by NO and the F10.7 index, thus providing a fundamental relationship between solar activity and the thermospheric cooling rate for use in thermospheric models. The change in NO radiated power is also consistent with changes in absorbed ultraviolet radiation over the same time period. Computations of radiated power using an empirical model show much less variability than observed by SABER.
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| 6. |
- Swarup, Kamal, et al.
(author)
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The auxin influx carrier LAX3 promotes lateral root emergence
- 2008
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In: Nature Cell Biology. - : Nature Publishing Group. - 1465-7392 .- 1476-4679. ; 10:8, s. 946-954
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Journal article (peer-reviewed)abstract
- Lateral roots originate deep within the parental root from a small number of founder cells at the periphery of vascular tissues and must emerge through intervening layers of tissues. We describe how the hormone auxin, which originates from the developing lateral root, acts as a local inductive signal which re-programmes adjacent cells. Auxin induces the expression of a previously uncharacterized auxin influx carrier LAX3 in cortical and epidermal cells directly overlaying new primordia. Increased LAX3 activity reinforces the auxin-dependent induction of a selection of cell-wall-remodelling enzymes, which are likely to promote cell separation in advance of developing lateral root primordia.
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| 7. |
- Szatmari, Peter, et al.
(author)
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Mapping autism risk loci using genetic linkage and chromosomal rearrangements.
- 2007
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 39:3, s. 319-328
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Journal article (peer-reviewed)abstract
- Autism spectrum disorders (ASDs) are common, heritable neurodevelopmental conditions. The genetic architecture of ASDs is complex, requiring large samples to overcome heterogeneity. Here we broaden coverage and sample size relative to other studies of ASDs by using Affymetrix 10K SNP arrays and 1,168 families with at least two affected individuals, performing the largest linkage scan to date while also analyzing copy number variation in these families. Linkage and copy number variation analyses implicate chromosome 11p12-p13 and neurexins, respectively, among other candidate loci. Neurexins team with previously implicated neuroligins for glutamatergic synaptogenesis, highlighting glutamate-related genes as promising candidates for contributing to ASDs.
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