Comparison of common burden tests for genetic association studies of rare variants.

Common burden tests have different statistical performance in genetic association studies of rare variants. Here, we compare the statistical performance of burden tests, such as CMC, WST, SUM and extension methods, using the computer-simulated datasets of rare variants with different parameters of sample sizes, linkage disequilibrium (LD), and different numbers of mixed non-associated variants. The simulation results showed that the type I error for all methods is near 0.05. When the rare variants had the same direction of effect, the higher LD and the less non-associated variants, the higher the power of these method, except the data adaptive SUM test. When the direction was different, the power was significantly reduced for all methods. The methods that consider the direction yielded larger statistical power than those methods without considering the effect direction, except the strong LD condition. And the larger the sample size, the larger the power. The statistical performance of burden tests is affected by a variety of factors, including the sample size, effect direction of variants, non-associated variants, and LD. Therefore, when choosing the method and setting the collection unit and weight, the prior biological information of genetic variation should be integrated to improve study efficiency.

Improvement of acetic acid tolerance and fermentation performance of Saccharomyces cerevisiae by disruption of the FPS1 aquaglyceroporin gene.

The FPS1 gene coding for the Fps1p aquaglyceroporin protein of an industrial strain of Saccharomyces cerevisiae was disrupted by inserting CUP1 gene. Wild-type strain, CE25, could only grow on YPD medium containing less than 0.45% (v/v) acetic acid, while recombinant strain T12 with FPS1 disruption could grow on YPD medium with 0.6% (v/v) acetic acid. Under 0.4% (v/v) acetic acid stress (pH 4.26), ethanol production and cell growth rates of T12 were 1.7 ± 0.1 and 0.061 ± 0.003 g/l h, while those of CE25 were 1.2 ± 0.1 and 0.048 ± 0.003 g/l h, respectively. FPS1 gene disruption in an industrial ethanologenic yeast thus increases cell growth and ethanol yield under acetic acid stress, which suggests the potential utility of FPS1 gene disruption for bioethanol production from renewable resources such as lignocelluloses.

Association between factors related to family planning/sexual and reproductive health and contraceptive use as well as consistent condom use among internal migrant population of reproductive ages in three cities in China, based on Heckprobit selection models.

OBJECTIVE: With the increased population mobility and the transition in population policy, scholars are quite concerned about family planning/sexual and reproductive health (SRH) and related factors among internal migrant population of reproductive age. Therefore, the proposed study was designed to explore the association between factors related to family planning/SRH and contraceptive use as well as consistent condom use among the above-described population in China. DESIGN: Cross-sectional study. SETTING: Three municipalities in China, namely Beijing, Shanghai and Chongqing. PARTICIPANTS: Among the 6545 participants, 2099, 2414 and 2031 subjects came from Beijing, Shanghai and Chongqing, respectively. RESULTS: A total of 6545 eligible participants were included as the full sample, 6188 of whom who had intercourse in the last 3 months were selected as the subsample. Among the subsample, 80.88% (5005/6188) adopted any form of contraceptive methods and 49.14% (3041/6188) consistently used condom in the last three sexual intercourses. Meanwhile, the involved participants had a better mastery of knowledge on SRH than on contraception (p<0.0001). The results of the Heckprobit models revealed that the factors associated with both contraceptive use and consistent condom use were relationship with the first intercourse partner, communication frequency with spouse/sexual partners on sex, actual number of children and knowledge on SRH, while knowledge on contraception and age at first intercourse were associated with contraceptive use and consistent condom use, respectively (p<0.05). CONCLUSIONS: In the current study, we revealed a high-level contraceptive prevalence, a relatively low-level consistent condom use and a poor mastery of knowledge on contraception and SRH. The Heckprobit selection model specified the existence of selection bias, providing evidence on the association between the factors on family planning/SRH and contraceptive use as well as consistent condom use, respectively. Our findings indicated that health institutions should offer appropriate technology and high-quality family planning/SRH services for the internal migrant population in China.

[Non-parametric Bootstrap estimation on the intraclass correlation coefficient generated from quantitative hierarchical data].

This paper aims to achieve Bootstraping in hierarchical data and to provide a method for the estimation on confidence interval(CI) of intraclass correlation coefficient(ICC).First, we utilize the mixed-effects model to estimate data from ICC of repeated measurement and from the two-stage sampling. Then, we use Bootstrap method to estimate CI from related ICCs. Finally, the influences of different Bootstraping strategies to ICC's CIs are compared. The repeated measurement instance show that the CI of cluster Bootsraping containing the true ICC value. However, when ignoring the hierarchy characteristics of data, the random Bootsraping method shows that it has the invalid CI. Result from the two-stage instance shows that bias observed between cluster Bootstraping's ICC means while the ICC of the original sample is the smallest, but with wide CI. It is necessary to consider the structure of data as important, when hierarchical data is being resampled. Bootstrapping seems to be better on the higher than that on lower levels.

Microsatellite primers for Halophila ovalis and cross-amplification in H. minor (Hydrocharitaceae).

UNLABELLED: • PREMISE OF THE STUDY: Polymorphic microsatellite primers were developed in the seagrass Halophila ovalis to investigate genetic variation. • METHODS AND RESULTS: Ten polymorphic microsatellite loci were developed in Halophila ovalis. The number of alleles per locus ranged from 2 to 12 across 80 H. ovalis individuals. These loci were successfully amplified in H. minor, and four were monomorphic across 30 individuals. • CONCLUSIONS: These results from four H. ovalis populations and one H. minor population show the broad utility of microsatellite loci in future studies of population genetics. Four distinct alleles were present in H. minor but absent in H. ovalis, indicating potential divergence between them.