Recessive/dominant model: Alternative choice in case-control-based genome-wide association studies.

An additive genetic model is usually employed in case-control-based genome-wide association studies. The model usually encodes "AA", "Aa" and "aa" ("a" represents the minor allele) as three different numbers, implying the contribution of genotype "Aa" to the phenotype is different from "AA" and "aa". From the perspective of biological phenomena, the coding is reasonable since the phenotypes of lives are not "black and white". A case-control based study, however, has only two phenotypes, case and control, which means that the phenotypes are "black and white". It suggests that a recessive/dominant model may be an alternative to the additive model. In order to investigate whether the alternative is feasible, we conducted comparative experiments on several models used in those studies through chi-square test and logistic regression. Our simulation experiments demonstrate that a recessive model is better than the additive model. The area under the curve of the former has increased by 5% compared with the latter, the discrimination of identifying risk single nucleotide polymorphisms has been improved by 61%, and the precision has also reached 1.10 times that of the latter. Furthermore, the real data experiments show that the precision and area under the curve of the former are 16% and 20% higher than the latter respectively, and the area under the curve of dominant model of the former is 13% higher than the latter. The results indicate a recessive/dominant model may be an alternative to the additive model and suggest a new route for case-control-based studies.

coPLINK: A complementary tool to PLINK.

In genome-wide association studies (GWAS), a wide variety of analysis tools have been designed, leading to various formats of GWAS data. How to convert a dataset in non-PLINK format into PLINK format to use its powerful analysis performance, or to convert a dataset in PLINK format into the format of other analysis tools, is a problem that needs to be faced and solved. To address this issue, we developed a tool called coPLINK, a complementary tool to PLINK, to cooperate with PLINK to implement the conversions of GWAS data formats and to provide some additional functions, such as data files comparison. The tool can implement mutual conversions not only between an existing data format and PLINK PED/BED, but also between a user-defined data format and PLINK PED. The usage and performance of the tool are similar to PLINK. The characteristics of the conversions of existing data formats and user-defined formats make it be a good assistant to PLINK or other tools and, have good potential for GWAS studies or other works.

Density distribution of gene expression profiles and evaluation of using maximal information coefficient to identify differentially expressed genes.

The hypothesis of data probability density distributions has many effects on the design of a new statistical method. Based on the analysis of a group of real gene expression profiles, this study reveal that the primary density distributions of the real profiles are normal/log-normal and t distributions, accounting for 80% and 19% respectively. According to these distributions, we generated a series of simulation data to make a more comprehensive assessment for a novel statistical method, maximal information coefficient (MIC). The results show that MIC is not only in the top tier in the overall performance of identifying differentially expressed genes, but also exhibits a better adaptability and an excellent noise immunity in comparison with the existing methods.

Biocomputional construction of a gene network under acid stress in Synechocystis sp. PCC 6803.

Acid stress is one of the most serious threats that cyanobacteria have to face, and it has an impact at all levels from genome to phenotype. However, very little is known about the detailed response mechanism to acid stress in this species. We present here a general analysis of the gene regulatory network of Synechocystis sp. PCC 6803 in response to acid stress using comparative genome analysis and biocomputational prediction. In this study, we collected 85 genes and used them as an initial template to predict new genes through co-regulation, protein-protein interactions and the phylogenetic profile, and 179 new genes were obtained to form a complete template. In addition, we found that 11 enriched pathways such as glycolysis are closely related to the acid stress response. Finally, we constructed a regulatory network for the intricate relationship of these genes and summarize the key steps in response to acid stress. This is the first time a bioinformatic approach has been taken systematically to gene interactions in cyanobacteria and the elaboration of their cell metabolism and regulatory pathways under acid stress, which is more efficient than a traditional experimental study. The results also provide theoretical support for similar research into environmental stresses in cyanobacteria and possible industrial applications.

[Effect of polycythemia on hypoxia induced pulmonary hypertension and pulmonary vascular remodeling in rats].

OBJECTIVE: To investigate the effect of polycythemia on hypoxia induced pulmonary hypertension and pulmonary vascular remodeling in rats. METHODS: The healthy female Sprague-Dawley rats were randomly divided into 3 groups: normoxia control group (C group), hypoxia group (H group), hypoxia + different doses of human recombine hemopoietin (rEPO) group. All rats in hyoxia groups were exposed to hypoxia, 8 hours every day, for 21 days. The rEPO groups were injected sc with different doses of rEPO (300 U/kg, 600 U/kg, 900 U/kg, 1200 U/kg) thrice weekly. Blood samples were taken for the measurement of RBC, Hb, Hct, plasma EPO concentration, whole blood/plasma viscosities, the animals were then catheterized to record mean pulmonary arterial pressure (mPAP) and demised to calculate the ratio [RV/(LV+S)]. Percentage of vascular wall thickness and muscularization of non-muscular pulmonary arteriole were examined microscopically. RESULTS: (1) As the dosage of exogenous rEPO increased, blood concentration of EPO increased correspondingly, as RBC, Hb, Hct and whole blood/plasma viscosities increased in various degrees. (2) There was positive correlation between whole blood viscosity and Hct at both high and low shears and linear correlation between mPAP and whole blood viscosity at high shear. (3) The degree of pulmonary hypertension, reflected by mPAP increased in accordance to rEPO dosage increment. However, the extent of pulmonary vascular remodeling alleviated somehow as the rEPO dose increased and so did right ventricular hypertrophy. CONCLUSION: Polycythemia induced by exogenous EPO increases the blood viscosity and the pulmonary vascular resistance, which contributes to the formation of hypoxia induced pulmonary hypertension.

[Changes of MMP-2,9 and TIMP-1 expressions in rats with pulmonary arterial hypertension after captopril and losartan interventions].

OBJECTIVE: To determine the effect of captopril and losartan on the expressions of matrix metalloproteinase-2,9 (MMP-2,9) and metalloproteinase-1 (TIMP-1) in rats with pulmonary arterial hypertension, and the mechanisms of captopril and losartan in intervening the development of pulmonary arterial hypertension. METHODS: Forty male Spraque-Dawley rats were divided into 4 groups randomly: pulmonary arterial hypertension (created by pneumonectomy plus MCT injection) model group (PAH Model), PAH model treated with captopril [PAH+Cap 10 mg/(kg x d)], losartan group [PAH+Los 15 mg/(kg x d)] and normal control group(Control). The mPAP, weight ratio of RV to LV+S, neointima formation, relative thickness of small pulmonary arteries, and degree of muscularization of non-muscular arterioles were measured at day 35. The expression of SM-a-actin in the PASMC was determined by immunochemistry stain. The expressions of MMP-2, 9, TIMP-1 and MMP-2, 9, TIMP-1 mRNA in the pulmonary tissues were determined by immunohistochemistry and FQ-PCR respectively. The enzymatic activity of MMP-2, 9 was measured by Gelatin zymography. RESULTS: Pneumonectomy plus MCT injection induced severe pulmonary arterial hypertension characterized by neointimal formation. Captopril or losartan suppressed the increase of mPAP, right ventricle weight, thickness of small pulmonary arteries and muscularization of peripheral pulmonary arterioles in the rats with PAH (P < 0.05). The PAH model group had higher expressions of MMP-2, 9, TIMP-1 mRNA and enzymatic activity of MMP-2, 9 in lung tissue than the other groups (P < 0.05). Captopril intervention had similar effects as losartan intervention. CONCLUSION: The captopril and losartan induced attenuation of PAH and pulmonary vascular remodeling is likely to be associated with the regulation of the expressions of MMP-2, 9, TIMP-1.