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Genes, Volume 7, Issue 1 (January 2016) – 4 articles

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Editorial
Acknowledgement to Reviewers of Genes in 2015
Genes 2016, 7(1), 4; https://0-doi-org.brum.beds.ac.uk/10.3390/genes7010004 - 21 Jan 2016
Viewed by 1821
Abstract
The editors of Genes would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2015. [...] Full article
Article
Long-Term Monitoring of Field Trial Sites with Genetically Modified Oilseed Rape (Brassica napus L.) in Saxony-Anhalt, Germany. Fifteen Years Persistence to Date but No Spatial Dispersion
Genes 2016, 7(1), 3; https://doi.org/10.3390/genes7010003 - 16 Jan 2016
Cited by 6 | Viewed by 3762
Abstract
Oilseed rape is known to persist in arable fields because of its ability to develop secondary seed dormancy in certain agronomic and environmental conditions. If conditions change, rapeseeds are able to germinate up to 10 years later to build volunteers in ensuing crops. [...] Read more.
Oilseed rape is known to persist in arable fields because of its ability to develop secondary seed dormancy in certain agronomic and environmental conditions. If conditions change, rapeseeds are able to germinate up to 10 years later to build volunteers in ensuing crops. Extrapolations of experimental data acted on the assumption of persistence periods for more than 20 years after last harvest of rapeseed. Genetically-modified oilseed rape—cultivated widely in Northern America since 1996—is assumed not to differ from its conventional form in this property. Here, experimental data are reported from official monitoring activities that verify these assumptions. At two former field trial sites in Saxony-Anhalt genetically-modified herbicide-resistant oilseed rape volunteers are found up to fifteen years after harvest. Nevertheless, spatial dispersion or establishment of GM plants outside of the field sites was not observed within this period. Full article
(This article belongs to the Section Population and Evolutionary Genetics and Genomics)
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Article
Detecting the Common and Individual Effects of Rare Variants on Quantitative Traits by Using Extreme Phenotype Sampling
Genes 2016, 7(1), 2; https://0-doi-org.brum.beds.ac.uk/10.3390/genes7010002 - 14 Jan 2016
Cited by 4 | Viewed by 2474
Abstract
Next-generation sequencing technology has made it possible to detect rare genetic variants associated with complex human traits. In recent literature, various methods specifically designed for rare variants are proposed. These tests can be broadly classified into burden and nonburden tests. In this paper, [...] Read more.
Next-generation sequencing technology has made it possible to detect rare genetic variants associated with complex human traits. In recent literature, various methods specifically designed for rare variants are proposed. These tests can be broadly classified into burden and nonburden tests. In this paper, we take advantage of the burden and nonburden tests, and consider the common effect and the individual deviations from the common effect. To achieve robustness, we use two methods of combining p-values, Fisher’s method and the minimum-p method. In rare variant association studies, to improve the power of the tests, we explore the advantage of the extreme phenotype sampling. At first, we dichotomize the continuous phenotypes before analysis, and the two extremes are treated as two different groups representing a dichotomous phenotype. We next compare the powers of several methods based on extreme phenotype sampling and random sampling. Extensive simulation studies show that our proposed methods by using extreme phenotype sampling are the most powerful or very close to the most powerful one in various settings of true models when the same sample size is used. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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Communication
Analysis of DNA Methylation and Hydroxymethylation in the Genome of Crustacean Daphnia pulex
Genes 2016, 7(1), 1; https://0-doi-org.brum.beds.ac.uk/10.3390/genes7010001 - 31 Dec 2015
Cited by 15 | Viewed by 3528
Abstract
The aim of our study was to analyze the presence of 5-methyl-cytosine (5-mC) and 5-hydroxymethyl-cytosine (5-hmC) in the genome of crustacean Daphnia pulex. First, the presence of 5-mC and 5-hmC in genomic DNA was demonstrated by using antibodies specific to either 5-mC [...] Read more.
The aim of our study was to analyze the presence of 5-methyl-cytosine (5-mC) and 5-hydroxymethyl-cytosine (5-hmC) in the genome of crustacean Daphnia pulex. First, the presence of 5-mC and 5-hmC in genomic DNA was demonstrated by using antibodies specific to either 5-mC or 5-hmC. Then, analysis of 5-mC and 5-hmC using pairs of restriction enzymes with different sensitivity to methylation and hydroxymethylation confirmed the presence of both modifications in selected regions of three genes (Cox4, Cand2 and Ephx1). To get a detailed picture of 5-hmC distribution over the D. pulex genome, we performed 5-hmC enrichment and sequenced the enriched fraction using next generation sequencing and non-enriched library (input) as a control. Comparison of input and enriched libraries showed that 5-hmC in exons is twice as frequent as in introns. Functional analysis indicated that 5-hmC abundance is associated with genes that are involved in the adenylate cyclase-activating G-protein-coupled receptor signaling pathway, molting cycles, morphogenesis and cell fate determination. Genes that lack 5-hmC tend to be involved in the regulation of the transforming growth factor beta receptor signaling pathway and in many mRNA-related processes. Our results suggest that epigenetic modifications are present in the genome of D. pulex and most likely are involved in the regulation of gene expression of this crustacean. Full article
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