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排序方式: 共有168条查询结果,搜索用时 31 毫秒
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Detecting non-neutral heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence 总被引:11,自引:4,他引:7
Natural selection, in the form of balancing selection or selective sweeps,
can result in a decoupling of the amounts of molecular polymorphism and
divergence. Thus natural selection can cause some areas of DNA sequence to
have greater silent polymorphism, relative to divergence between species,
than other areas. It would be useful to have a statistical test for
heterogeneity in the polymorphism to divergence ratio across a region of
DNA sequence, one that could identify heterogeneity greater than that
expected from the neutral processes of mutation, drift, and recombination.
The only currently available test requires that a region be arbitrarily
divided into sections that are compared with each other, and the
subjectivity of this division could be problematic. Here a test is proposed
in which runs of polymorphic and fixed sites are counted, where a "run" is
a set of one or more sites of one type preceded and followed by the other
type. The number of runs is smaller than otherwise expected if
polymorphisms are clumped together. By simulating neutral evolution and
comparing the observed number of runs to the simulations, a statistical
test is possible which does not require any a priori decisions about
subdivision.
相似文献
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M Ehrich J E Aswell R L van Tassell T D Wilkins A R Walker N J Richardson 《Mutation research》1979,64(4):231-240
The incidence of mutagens in the feces of 3 South-African populations at different risk levels for colon cancer has been determined. Lyophilized fecal samples were extracted with ether and the mutagenicity of the extracts determined using the Salmonella/mammalian microsome mutagenicity test. 19% of the samples from urban white South-Africans, a population at a high risk for colon cancer, were mutagenic using Salmonella typhimurium strain TA100. This incidence was significantly greater (p less than 0.001) than the incidence of mutagen excretion in the low-risk populations of urban blacks (2%) and rural blacks (0%). This pattern was also obtained using Salmonella typhimurium strain TA98. The incidence of mutagen excretion for urban whites was 10%, as compared to 5% and 2% for urban and rural blacks, respectively. 相似文献
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Taylor J. Jensen Tricia Zwiefelhofer Roger C. Tim ?eljko D?akula Sung K. Kim Amin R. Mazloom Zhanyang Zhu John Tynan Tim Lu Graham McLennan Glenn E. Palomaki Jacob A. Canick Paul Oeth Cosmin Deciu Dirk van den Boom Mathias Ehrich 《PloS one》2013,8(3)
Background
Circulating cell-free (ccf) fetal DNA comprises 3–20% of all the cell-free DNA present in maternal plasma. Numerous research and clinical studies have described the analysis of ccf DNA using next generation sequencing for the detection of fetal aneuploidies with high sensitivity and specificity. We sought to extend the utility of this approach by assessing semi-automated library preparation, higher sample multiplexing during sequencing, and improved bioinformatic tools to enable a higher throughput, more efficient assay while maintaining or improving clinical performance.Methods
Whole blood (10mL) was collected from pregnant female donors and plasma separated using centrifugation. Ccf DNA was extracted using column-based methods. Libraries were prepared using an optimized semi-automated library preparation method and sequenced on an Illumina HiSeq2000 sequencer in a 12-plex format. Z-scores were calculated for affected chromosomes using a robust method after normalization and genomic segment filtering. Classification was based upon a standard normal transformed cutoff value of z = 3 for chromosome 21 and z = 3.95 for chromosomes 18 and 13.Results
Two parallel assay development studies using a total of more than 1900 ccf DNA samples were performed to evaluate the technical feasibility of automating library preparation and increasing the sample multiplexing level. These processes were subsequently combined and a study of 1587 samples was completed to verify the stability of the process-optimized assay. Finally, an unblinded clinical evaluation of 1269 euploid and aneuploid samples utilizing this high-throughput assay coupled to improved bioinformatic procedures was performed. We were able to correctly detect all aneuploid cases with extremely low false positive rates of 0.09%, <0.01%, and 0.08% for trisomies 21, 18, and 13, respectively.Conclusions
These data suggest that the developed laboratory methods in concert with improved bioinformatic approaches enable higher sample throughput while maintaining high classification accuracy. 相似文献8.
Janine JH Oosterhof G Jolanda Elving Ietse Stokroos Arie van nieuw Amerongen Henny C van der Mei Henk J Busscher 《Biofouling》2013,29(6):347-353
The integrity of biofilms on voice prostheses used to rehabilitate speech in laryngectomized patients causes unwanted increases in airflow resistance, impeding speech. Biofilm integrity is ensured by extracellular polymeric substances (EPS). This study aimed to determine whether synthetic salivary peptides or mucolytics, including N-acetylcysteine and ascorbic acid, influence the integrity of voice prosthetic biofilms. Biofilms were grown on voice prostheses in an artificial throat model and exposed to synthetic salivary peptides, mucolytics and two different antiseptics (chlorhexidine and Triclosan). Synthetic salivary peptides did not reduce the air flow resistance of voice prostheses after biofilm formation. Although both chlorhexidine and Triclosan reduced microbial numbers on the prostheses, only the Triclosan-containing positive control reduced the air flow resistance. Unlike ascorbic acid, the mucolytic N-acetylcysteine removed most EPS from the biofilms and induced a decrease in air flow resistance. 相似文献
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Good‐bye to tropical alpine plant giants under warmer climates? Loss of range and genetic diversity in Lobelia rhynchopetalum 下载免费PDF全文
Desalegn Chala Christian Brochmann Achilleas Psomas Dorothee Ehrich Abel Gizaw Catherine A. Masao Vegar Bakkestuen Niklaus E. Zimmermann 《Ecology and evolution》2016,6(24):8931-8941
The main aim of this paper is to address consequences of climate warming on loss of habitat and genetic diversity in the enigmatic tropical alpine giant rosette plants using the Ethiopian endemic Lobelia rhynchopetalum as a model. We modeled the habitat suitability of L. rhynchopetalum and assessed how its range is affected under two climate models and four emission scenarios. We used three statistical algorithms calibrated to represent two different complexity levels of the response. We analyzed genetic diversity using amplified fragment length polymorphisms and assessed the impact of the projected range loss. Under all model and scenario combinations and consistent across algorithms and complexity levels, this afro‐alpine flagship species faces massive range reduction. Only 3.4% of its habitat seems to remain suitable on average by 2,080, resulting in loss of 82% (CI 75%–87%) of its genetic diversity. The remaining suitable habitat is projected to be fragmented among and reduced to four mountain peaks, further deteriorating the probability of long‐term sustainability of viable populations. Because of the similar morphological and physiological traits developed through convergent evolution by tropical alpine giant rosette plants in response to diurnal freeze‐thaw cycles, they most likely respond to climate change in a similar way as our study species. We conclude that specialized high‐alpine giant rosette plants, such as L. rhynchopetalum, are likely to face very high risk of extinction following climate warming. 相似文献
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