Analysis Of Genotype Combinations Research Articles

Genetic Associations of Plasminogen Activator Inhibitor-1-Related miRNA Variants with Coronary Artery Disease.

Coronary artery disease (CAD) is one of the most common types of cardiovascular disease and can lead to a heart attack as plaque gradually builds up inside the coronary arteries, blocking blood flow. Previous studies have shown that polymorphisms in the PAI-1 gene are associated with CAD; however, studies of the PAI-1 3'-untranslated region, containing a miRNA binding site, and the miRNAs that interact with it, are insufficient. To investigate the association between miRNA polymorphisms and CAD in the Korean population based on post-transcriptional regulation, we genotyped five polymorphisms in four miRNAs targeting the 3'-untranslated region of PAI-1 using real-time PCR and TaqMan assays. We found that the mutant genotype of miR-30c rs928508 A > G was strongly associated with increased CAD susceptibility. In a genotype combination analysis, the combination of the homozygous mutant genotype (GG) of miR-30c rs928508 with the wild-type genotype (GG) of miR-143 rs41291957 resulted in increased risk for CAD. Also, in an allele combination analysis, the combination of the mutant allele (G) of miR-30c rs928508 and the wild-type allele (G) of miR-143 rs41291957 resulted in increased risk for CAD. Furthermore, metabolic syndrome and diabetes mellitus showed synergistic effects on CAD risk when combined with miR-30c rs928508. These results can be applied to identify CAD prognostic biomarkers among miRNA polymorphisms and various clinical factors.

Association of Polymorphisms in FSHR, INHA, ESR1, and BMP15 with Recurrent Implantation Failure.

Recurrent implantation failure (RIF) refers to two or more unsuccessful in vitro fertilization embryo transfers in the same individual. Embryonic characteristics, immunological factors, and coagulation factors are known to be the causes of RIF. Genetic factors have also been reported to be involved in the occurrence of RIF, and some single nucleotide polymorphisms (SNPs) may contribute to RIF. We examined SNPs in FSHR, INHA, ESR1, and BMP15, which have been associated with primary ovarian failure. A cohort of 133 RIF patients and 317 healthy controls consisting of all Korean women was included. Genotyping was performed by Taq-Man genotyping assays to determine the frequency of the following polymorphisms: FSHR rs6165, INHA rs11893842 and rs35118453, ESR1 rs9340799 and rs2234693, and BMP15 rs17003221 and rs3810682. The differences in these SNPs were compared between the patient and control groups. Our results demonstrate a decreased prevalence of RIF in subjects with the FSHR rs6165 A>G polymorphism [AA vs. AG adjusted odds ratio (AOR) = 0.432; confidence interval (CI) = 0.206-0.908; p = 0.027, AA+AG vs. GG AOR = 0.434; CI = 0.213-0.885; p = 0.022]. Based on a genotype combination analysis, the GG/AA (FSHR rs6165/ESR1 rs9340799: OR = 0.250; CI = 0.072-0.874; p = 0.030) and GG-CC (FSHR rs6165/BMP15 rs3810682: OR = 0.466; CI = 0.220-0.987; p = 0.046) alleles were also associated with a decreased RIF risk. Additionally, the FSHR rs6165GG and BMP15 rs17003221TT+TC genotype combination was associated with a decreased RIF risk (OR = 0.430; CI = 0.210-0.877; p = 0.020) and increased FSH levels, as assessed by an analysis of variance. The FSHR rs6165 polymorphism and genotype combinations are significantly associated with RIF development in Korean women.

Study of the Association between VEGF Polymorphisms and the Risk of Coronary Artery Disease in Koreans.

Coronary artery disease (CAD), a leading cause of death worldwide, has a complex etiology comprising both traditional risk factors (type 2 diabetes, dyslipidemia, arterial hypertension, and cigarette smoking) and genetic factors. Vascular endothelial growth factor (VEGF) notably contributes to angiogenesis and endothelial homeostasis. However, little is known about the relationship between CAD and VEGF polymorphisms in Koreans. The aim of this study is to investigate the associations of 2 VEGF promoter region polymorphisms (−1154G>A [rs1570360], −1498T>C [rs833061]) and 4 VEGF 3′-UTR polymorphisms (+936C>T [rs3025039], +1451C>T [rs3025040], +1612G>A [rs10434], and +1725G>A [rs3025053]) with CAD susceptibility in Koreans. We studied 885 subjects: 463 CAD patients and 422 controls. Genotyping was conducted with polymerase chain reaction-restriction fragment length polymorphism analysis and TaqMan allelic discrimination assays, and the genotype frequencies were calculated. We then performed haplotype and genotype combination analyses and measured the associations between VEGF polymorphisms and clinical variables in both the CAD patients and control subjects. We detected statistically significant associations between CAD and certain VEGF allele combinations. In the haplotypes of 5 single-nucleotide polymorphisms, the VEGF allele combination −1154A/+936T was associated with a decreased prevalence of CAD (A-T-T-G-G of VEGF −1154G>A/−1498T>C/+936C>T/+1612G>A/+1725G>A, AOR = 0.077, p = 0.021). In contrast, the VEGF allele combinations −1498T/+1725A and −1498T/+1612A/+1725A were associated with an increased prevalence of CAD (G-T-C-C-A of VEGF −1154G>A/−1498T>C/+936C>T/+1451C>T/+1725G>A, AOR = 1.602, p = 0.047; T-C-C-A-A of VEGF −1498T>C/+936C>T/+1451C>T/+1612G>A/+1725G>A, AOR = 1.582, p = 0.045). Gene–environment combinatorial analysis showed that the combination of the VEGF +1725AA genotype and several clinical factors (e.g., body mass index, hemoglobin A1c, and low-density lipoprotein cholesterol) increased the risk of CAD. Therefore, we suggest that VEGF polymorphisms and clinical factors may impact CAD prevalence.

Association of VEGF -2549 I/D and VEGF +936 C/T Polymorphisms with Chronic Kidney Disease in North-West Indian Patients.

Chronic kidney disease (CKD) is a complex multifactorial disease in which both genetic and environmental factors influence the onset, development and progression of disease. The genetic variations in the vascular endothelial growth factor (VEGF) can influence levels of VEGF protein expression, and thus, susceptibility to progression of kidney diseases. The aim of the present study was to evaluate the association of VEGF-2549 I/D and VEGF +936 C/T polymorphisms in CKD stage V patients from North-West India. In this case-control study, 166 patients and 166 controls were analyzed. DNA samples were screened for VEGF -2549I/D and VEGF +936 C/T polymorphisms using polymerase chain reaction-based (PCR) methods. The genotype frequency of VEGF -2549 I/D was significantly different between patients and controls (P < 0.05). ID genotype of VEGF -2549 I/D polymorphism was significantly associated with decreased risk of CKD (P = 0.009). Genetic model analysis of VEGF -2549 I/D polymorphism revealed a significantly decreased risk of CKD in co-dominant (P = 0.009), dominant (P = 0.021), and over-dominant (P = 0.012) models. Genotype and allele frequency of VEGF +936 C/T polymorphism was not significantly different between the patient and control groups. Genotype combination analysis revealed that ID-CT genotype combination of VEGF -2549 I/D and VEGF +936 C/T polymorphisms was associated with decreased CKD risk (P = 0.047). VEGF -2549 ID genotype and ID-CT genotype combination of VEGF -2549 I/D and VEGF +936 C/T polymorphisms was significantly associated with reduced CKD risk in North-West Indians.

Study of the Association Between microRNA (miR-25T>C, miR-32C>A, miR-125C>T, and miR-222G>T) Polymorphisms and the Risk of Recurrent Pregnancy Loss in Korean Women.

Recurrent pregnancy loss (RPL), which is defined as two pregnancy losses that occur before 20 weeks of gestation, is relatively common, occurring in approximately 1–5% of women. The underlying cause is often unclear, although numerous factors may contribute to RPL, including environmental and immunological factors, blood coagulation disorders, and genetics. In particular, single nucleotide variants have been associated with RPL, including those found in microRNAs (miRNAs). We investigated the association between four miRNA polymorphisms, miR-25T>C, miR-32C>A, miR-125aC>T, and miR-222G>T, and RPL in a cohort consisting of 361 RPL patients and 272 controls. Subjects were genotyped at miRNA loci by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis, and genotype frequencies were calculated. We then performed allele and genotype combination analyses and measured the association between miRNA polymorphisms and clinical variables in both RPL patients and controls. We detected a statistically significant association between RPL and the miR-25T/miR-32C/miR-125aT/miR-222T allele combination (adjusted odds ratio (AOR), 4.361; 95% confidence interval (CI), 1.496–12.72; P = 0.003). Three-gene combinations, including miR-32C/miR-125aT/miR-222T (AOR, 3.085; 95% CI, 1.254–7.588; P = 0.010) and miR-25T/miR-125aT/miR-222T (AOR, 2.929; 95% CI, 1.183–7.257; P = 0.015), and the two-gene combination miR-125aT/miR-222T (AOR, 2.417; 95% CI, 1.084–5.386; P = 0.026) were also associated with RPL. Analysis of variance (ANOVA) revealed that platelet counts and blood urea nitrogen levels were significantly different in RPL patients expressing different miR-125aC>T and miR-25T>C genotypes, respectively (P < 0.05). In addition, creatinine levels were lower in RPL patients expressing the minor alleles miR-25T>C and miR-32C>A. We investigated miRNAs (miR-25, miR-32, miR-125a, miR-222) in RPL patients and healthy controls. Significantly different allele frequencies were detected by ANOVA. We suggest that miRNAs and clinical factors can impact RPL occurrence.

Association between microRNA machinery gene polymorphisms and recurrent implantation failure.

The present study aimed to investigate the potential association of five miRNA machinery gene polymorphisms (DICER1 rs3742330A>G, DROSHA rs10719T>C, RAN rs14035C>T, XPO5 rs11077A>C and DGCR8 rs417309G>A) with recurrent implantation failure (RIF), a clinical condition in which good-quality embryos repeatedly fail to implant following two or more in vitro fertilization cycles, and its associated risk factors in Korean women. Therefore, the present study performed genotype analysis and assessed the frequency of these miRNA gene polymorphisms in patients diagnosed with RIF (n=119) and randomly selected controls (n=210) with at least one live birth and no history of pregnancy loss. The DROSHA rs10719T>C and RAN rs14035C>T polymorphisms were identified to be significantly associated with decreased prevalence of RIF. Additionally, the DROSHA rs10719 TC and the RAN rs14035 CT genotypes were present at significantly lower frequencies in the RIF group than in the control group (adjusted odds ratio=0.550; 95% CI, 0.339-0.893; P=0.016; and adjusted odds ratio=0.590; 95% CI, 0.363-0.958; P=0.033, respectively). Furthermore, the combined RAN rs14035 CT+TT genotype was observed to be associated with decreased RIF prevalence (adjusted odds ratio=0.616; 95% CI, 0.386-0.982; P=0.042). Genotype combination analysis for the various miRNA polymorphisms revealed that the DROSHA TC genotype exhibited a highly significant negative association with RIF prevalence when combined with the RAN CT genotype (adjusted odds ratio=0.314; 95% CI, 0.147-0.673; P=0.003; false discovery rate-adjusted P=0.023). The present study revealed an association between the DROSHA rs10719 and RAN rs14035 3'UTR polymorphisms and decreased risk of RIF in Korean women, which suggests that these gene polymorphisms could represent potential markers for predicting RIF risk.

Acinetobacter pullicarnis sp. nov. isolated from chicken meat.

A novel bacterial strain, named S23T, was isolated from chicken meat of local market in Korea. Cells were Gram-negative, milky-yellow colored, non-motile and coccobacillus. The strain was obligate aerobic and catalase-positive, oxidase-negative, optimum growth temperature and pH were 25°C and pH 7.0, respectively. On the basis of 16S rRNA gene sequence analysis, strain S23T belongs to the genus Acinetobacter and is most closely related to Acinetobacter defluvii KCTC 52503T (97.40%). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) value between strain S23T and its closet phylogenetic neighbors was below 76% and 17%, respectively. The G + C content of genomic DNA of strain S23T was 41.53mol%. The major respiratory quinone was Q-9. The major cellular fatty acids were summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c), C18:1ω9c, and C16:0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanol-amine, and phosphatidylserine. The ANI and dDDH results and results of the genotypic analysis in combination with chemotaxonomic and physiological data demonstrated that strain S23T represented a novel species within the genus Acinetobacter, for which the name Acinetobacter pullicarnis sp. nov. is proposed. The strain type is S23T (= KACC 19921T = JCM 33150T).

Genetic polymorphisms of the cobalamin transport system are associated with idiopathic recurrent implantation failure.

Vitamin B12 (cobalamin, Cbl) plays a role in the recycling of folate, which is important in pregnancy. Transcobalamin II (TCN2) and transcobalamin receptor (TCblR) proteins are involved in the cellular uptake of Cbl. TCN2 binds Cbl in the plasma, and TCblR binds TCN2-Cbl at the cell surface. Therefore, we investigated the potential association between polymorphisms in Cbl transport proteins, TCN2 and TCblR, and recurrent implantation failure (RIF) susceptibility. The genotypes of TCN2 67A>G, TCN2 776C>G, and TCblR 1104C>T were determined for RIF patients and healthy controls using a polymerase chain reaction restriction fragment length polymorphism assay. Additionally, statistical analysis was performed to compare the genotype frequencies between RIF patients and controls. The TCN2 67 polymorphism AG type was associated with RIF risk. Some allele combinations that contained the TCN2 67 polymorphism G allele were associated with increased RIF risk, whereas other allele combinations that contained the TCblR 1104 polymorphism T alleles were associated with decreased RIF risk. In genotype combination analysis, two combinations containing the TCN2 67 polymorphism AG type were associated with RIF risk. Our study showed that the polymorphisms of TCN2 and TCblR are associated with RIF and are potential genetic predisposing factors for RIF among Korean women. Additionally, our findings support a potential role for TCN2 and TCblR in RIF among Korean women. However, further studies are required to investigate the role of the polymorphisms in those proteins and RIF because the roles of the TCN2 and TCblR polymorphisms in RIF are not clear.

Association Study between the Polymorphisms of Matrix Metalloproteinase (MMP) Genes and Idiopathic Recurrent Pregnancy Loss.

Recurrent pregnancy loss (RPL) refers to two or more consecutive pregnancy losses. It is estimated that fewer than 5% of women experience RPL. Matrix metalloproteinases (MMPs) are a family of proteolytic enzymes that play important roles in providing a safe and conducive environment for the stable development of the fetus. In this case-control study, we evaluated the associations between RPL and single nucleotide polymorphisms (SNPs) in MMP-8 and MMP-27. We recruited 375 Korean women with a history of RPL and 240 ethnically-matched healthy parous controls, and we performed genotyping for the MMP-8 rs2509013 C>T, MMP-8 rs11225395 G>A, and MMP-27 rs3809017 T>C polymorphisms. All SNPs were genotyped via the polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) assay. In the genotype frequency analyses, the TT genotype of the MMP-8 rs2509013 C>T (age-adjusted odds ratio, 0.415; 95% confidence interval, 0.257–0.671; P = 0.0003) and TC genotype of MMP-27 rs3809017 T>C (age-adjusted odds ratio, 0.681; 95% confidence interval, 0.483–0.961; P = 0.029) were associated with decreased RPL susceptibility. Moreover, these trends were maintained in the haplotype and genotype combination analyses. Interestingly, amongst the RPL patients, higher levels of homocysteine (P = 0.042) and uric acid (P = 0.046) were associated with MMP-27 rs3809017 T>C. In conclusion, the two polymorphisms of MMP-8 and MMP-27 were significantly associated with RPL risk, both individually and in combination. Therefore, these two polymorphisms are potential biomarkers for RPL susceptibility.

Sphingobium tyrosinilyticum sp. nov., a tyrosine hydrolyzing bacterium isolated from Korean radish garden.

A yellow-pigmented novel bacterial strain, MAH-12T, was isolated from a soil sample of Korean radish garden and was characterized using a polyphasic approach. Cells were Gram-staining negative, non-motile and rod-shaped. The strain was aerobic, catalase positive, optimum growth temperature and pH were 28-30°C and 6.0, respectively. The novel strain is able to hydrolyze L-tyrosine, starch, esculin and 4-nitrophenyl-β-D-galactopyranoside. On the basis of 16S rRNA gene sequence analysis, strain MAH-12T belongs to the genus Sphingobium and is most closely related to several Sphingobium type strains (97.2-97.8%). In DNA-DNA hybridization tests, the DNA relatedness between strain MAH-12T and its closest phylogenetic neighbors was below 45.0%. The DNA G + C content was 64.0mol% and the predominant respiratory quinone was ubiquinone-10. The major cellular fatty acids were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c) and C16:0. The DNA-DNA hybridization results and results of the genotypic analysis in combination with chemotaxonomic and physiological data demonstrated that strain MAH-12T represented a novel species within the genus Sphingobium, for which the name Sphingobium tyrosinilyticum is proposed. The type strain is MAH-12T (= KACC 19297T = CGMCC 1.16225T). The NCBI GenBank accession number for the 16S rRNA gene sequence of strain MAH-12T is KY964278 and the digital protologue database taxon number of strain MAH-12T is TA00463.

Luteibacter pinisoli sp. nov., a casein degrading bacterium isolated from rhizospheric soil of Pinus koraiensis.

A yellow pigmented, Gram-staining negative, motile and rod-shaped novel bacterial strain, designated MAH-14T was isolated from rhizospheric soil and was characterized using a polyphasic approach. The isolated strain was aerobic, oxidase and catalase were positive, optimum growth temperature and pH were 28-30°C and 6.5, respectively. The novel strain is able to hydrolyze casein, starch, esculin, gelatin, L-tyrosine, DNA, tween 80, tween 20, L-arginine and 4-nitrophenyl-BD-galactopyranoside. On the basis of 16S rRNA gene sequence analysis, strain MAH-14T belongs to the genus Luteibacter and is most closely related to Luteibacter yeojuensis R2A16-10T (98.5%), Luteibacter anthropi CCUG 25036T (98.4%) and Luteibacter rhizovicinus LJ96T (98.3%). In DNA-DNA hybridization experiments, the DNA relatedness between strain MAH-14T and its closest phylogenetic neighbor was below 45.0%. The predominant respiratory quinone and the DNA G + C content of the novel strain were ubiquinone-8 and 63.5mol%, respectively. The novel strain MAH-14T is able to produce flexirubin-type pigments. The major cellular fatty acids were C15:0 iso, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) and summed feature 9 (C17:1 iso ω9c and/or C16:0 10-methyl). The DNA-DNA hybridization results and results of the genotypic analysis in combination with chemotaxonomic and physiological data revealed that strain MAH-14T represented a novel species within the genus Luteibacter, for which the name Luteibacter pinisoli, is proposed. The type strain is MAH-14T (= KACC 19298T = CGMCC 1.16227T).

Chryseobacterium chungangensis sp. nov., a bacterium isolated from soil of sweet gourd garden.

A novel bacterial strain, named MAH-7T, was isolated from a soil sample of a Korean sweet gourd garden and was characterized using a polyphasic approach. Cells were Gram-staining negative, orange colored, non-motile and rod shaped. The strain was aerobic and catalase, oxidase positive, optimum growth temperature and pH were 28-30°C and 7.0, respectively. On the basis of 16S rRNA gene sequence analysis, strain MAH-7T belongs to the genus Chryseobacterium and is most closely related to Chryseobacterium formosense CC-H3-2T (97.96%) and Chryseobacterium zeae JM-1085T (97.19%). In DNA-DNA hybridization tests, the DNA relatedness between strain MAH-7T and its closest phylogenetic neighbors were below 45.0%. The DNA G+C content was 37.6mol% and the predominant respiratory quinone was menaquinone-6 (MK-6). Flexirubin-type pigments were found to be present. The major cellular fatty acids were C15:0 iso, C17:0 iso 3OH, C17:1 isoω9c and summed feature 3 (C16:1ω7c and/or C16:1ω6c). The DNA-DNA hybridization results and results of the genotypic analysis in combination with chemotaxonomic and physiological data demonstrated that strain MAH-7T represented a novel species within the genus Chryseobacterium, for which the name Chryseobacterium chungangensis is proposed. The type strain is MAH-7T (= KACC 19293T = CGMCC 1.16232T). The NCBI GenBank accession number for the 16S rRNA gene sequence of strain MAH-7T is KY964274.

Caenispirillum humi sp. nov., a bacterium isolated from the soil of Korean pine garden.

A novel bacterial strain MAH-8T was isolated from a soil sample of a Korean pine garden and was characterized using a polyphasic approach. Cells were Gram-staining negative, pinkish yellow colored, motile and vibrio-shaped. The strain was aerobic and catalase, oxidase positive, optimum growth temperature and pH were 28-30°C and 7.0, respectively. On the basis of 16S rRNA gene sequence analysis, strain MAH-8T belongs to the genus Caenispirillum and is most closely related to Caenispirillum bisanense KCTC 12839T (98.14%), Caenispirillum deserti KCTC 42064T (96.35%), and Caenispirillum salinarum JCM 17360T (95.76%). In DNA-DNA hybridization tests, the DNA relatedness between strain MAH-8T and its closest phylogenetic neighbor was below 45.0%. The DNA G + C content was 70.5mol% and the predominant respiratory quinone was ubiquinone-10. Flexirubin-type pigments were present and the major cellular fatty acids were C18:1 ω7c/C18:1 ω6c, C16:1 ω7c/C16:1 ω6c and C16:0. The results of DNA-DNA hybridization and genotypic analysis in combination with chemotaxonomic and physiological data demonstrated that strain MAH-8T represented a novel species within the genus Caenispirillum, for which the name Caenispirillum humi, is proposed. The type strain is MAH-8T (= KACC 19294T = CGMCC 1.16224T). The NCBI GenBank Accession Number for the 16S rRNA gene sequence of strain MAH-8T is KY964275.

Epigenetic and genetic variants in the HTR1B gene and clinical improvement in children and adolescents treated with fluoxetine

The serotonin 1B receptor (5-HT1B) is important to both the pathogenesis of major depressive disorder and the antidepressant effects of selective serotonin reuptake inhibitors. Although fluoxetine has been shown to be effective and safe in children and adolescents, not all patients experience a proper clinical response, which has led to further study into the main factors involved in this inter-individual variability. Our aim was to study the effect of epigenetic and genetic factors that could affect 5-hydroxytryptamine receptor 1B (HTR1B) gene expression, and thereby response to fluoxetine. A total of 83 children and adolescents were clinically assessed 12weeks after of initiating an antidepressant treatment with fluoxetine for the first time. We evaluated the influence of single nucleotide polymorphisms (SNPs) specifically located in transcription factor binding sites (TFBSs) on their clinical improvement. A combined genetic analysis considering the significant SNPs together with the functional variant rs130058 previously associated in our population was also performed. Moreover, we assessed, for the first time in the literature, whether methylation levels of the HTR1B promoter region could be associated with the pharmacological response. Two, rs9361233 and rs9361235, were significantly associated with clinical improvement after treatment with fluoxetine. The heterozygous genotype combination analysis showed a negative correlation with clinical improvement. The lowest improvement was experienced by patients who were heterozygous for all three SNPs. Moreover, a negative correlation was found between clinical improvement and the average methylation level of the HTR1B promoter. These results give new evidence for the role of epigenetic and genetic factors which could modulate HTR1B expression in the pharmacological response to antidepressants.

The Study of Associations of Polymorphisms of Candidate Gene of Cardiovascular Diseases With Reduction of Glomerular Filtration Rate in Patients With ST Segment Elevation Myocardial Infarction

to study associations of polymorphic genetic variants of inflammatory response, endothelial function, lipid metabolism, and blood coagulation with impaired renal function in patients with ST elevation myocardial infarction (STEMI). We enrolled in the study 171 patients admitted to the Kemerovo Cardiology Dispensary within 24 hours after onset of STEMI. All patients underwent genotype identification of 25 polymorphic variants of 18 major candidate genes for cardiovascular disease. Genotyping was performed with DNA chip SINKAR-1 (Institute of Medical Genetics and LLC "Genomic Diagnosis"). Glomerular filtration rate (GFR) was estimated using serum creatinine level measured at admission. Comparison of allelic and genotype frequencies of the studied polymorphisms revealed that angiotensin-converting enzyme (ACE) gene rs4291 was associated with decreased GFR: odds ratio (OR) for carriers of rare TT genotype was 2.31 [1.01-5.25], =0.043. Analysis of genotype combinations of ACE rs4343 polymorphism and hepatic lipase gene (LIPC) rs1800588 showed that AA genotype of rs4343 polymorphism in combination with CC genotype of rs1800588 polymorphism was associated with lowest risk of renal dysfunction, whereas GG and AG genotypes of ACE rs4343 in combination with TT and CT genotypes of LIPC rs1800588.

Pseudoxanthomonas humi sp. nov., a bacterium isolated from rhizospheric soil of Fraxinus chinensis in Gyeonggi Province, South Korea

A novel bacterial strain THG-MM13(T) was isolated from rhizospheric soil sample and was characterized by using a polyphasic approach. Cells were Gram-reaction-negative, non-motile and rod-shaped. The strain was aerobic, catalase and oxidase positive, and optimum growth temperature and pH were 28 °C and 7.0, respectively. On the basis of 16S rRNA gene sequence analysis, strain THG-MM13(T) (KM598260) belongs to the genus Pseudoxanthomonas and is most closely related to Pseudoxanthomonas wuyuanensis KCTC 23877(T) (97.4 %) (JN247803), followed by Pseudoxanthomonas koreensis KCTC 12208(T) (96.7 %) (AY550263) and Pseudoxanthomonas yeongjuensis KACC 11580(T) (96.7 %) (DQ438977). The DNA G + C content was 63.7 mol%, and the predominant respiratory quinone was ubiquinone-8. The major polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were iso-C15:0 (31.3 %) and iso-C16:0 (19.3 %). The DNA-DNA relatedness value between strain THG-MM13(T) and P. wuyuanensis KCTC 23877(T) was below 50 %. The DNA-DNA hybridization result and results of the genotypic analysis in combination with chemotaxonomic and physiological data demonstrated that strain THG-MM13(T) represented a novel species within the genus Pseudoxanthomonas, for which the name Pseudoxanthomonas humi is proposed. The type strain is THG-MM13(T) (=KACC 18280(T) = CCTCC AB 2015122(T)).

Genetic polymorphisms of the BMAP-28 and MASP-2 genes and their correlation with the somatic cell score in Chinese Holstein cattle.

DNA sequencing, nested polymerase chain reaction (PCR), and PCR-restriction fragment length polymorphism were used to investigate mutations in the coding regions of the bovine myeloid antimicrobial peptide-28 (BMAP-28) and mannan-binding lectin-associated serine protease-2 (MASP-2) genes in 249 Chinese Holstein dairy cows. The associations between the polymorphisms and somatic cell score (SCS) were analyzed to determine the potential of these genes as genetic markers for breeding mastitis-resistant dairy cattle. The results revealed a C-86G synonymous mutation in the BMAP-28 gene that caused no alteration in the amino acid sequence. G553A mutation was found in the MASP-2 gene that led to the substitution of glycine with serine. The chi-square test showed that the G553A mutation was in Hardy-Weinberg equilibrium in the Chinese Holstein dairy cows, whereas the C-86G mutation was not. The variance analysis of the influence of group loci and different genotypes on the SCS showed that the SCS of genotype CC was significantly lower than those of genotypes CG and GG (P < 0.05) of the C-86G mutation, and that the SCS of genotype GG was significantly lower than those of genotypes GA and AA (P < 0.05) of the G553A mutation. Genotype combination analysis showed that the combination of the BMAP-28 genotype CC and the MASP-2 genotype GG was the best one, in which the SCS was significantly lower than those in the other combinations. Thus, this combination might be useful as a molecular and genetic marker of mastitis in Chinese Holstein dairy cows.

Paenibacillus ginsengiterrae sp. nov., a ginsenoside-hydrolyzing bacteria isolated from soil of ginseng field.

A novel bacterial strain DCY89(T) was isolated from soil sample of ginseng field and was characterized using a polyphasic approach. Cells were Gram-reaction-positive, rod-shaped, spore-forming and motile with flagella. The strain was aerobic, esculin and starch positive, catalase- and oxidase-negative, optimum growth temperature, and pH were 25-30°C and 6.0-7.5, respectively. On the basis of 16S rRNA gene sequence analysis, strain DCY89(T) was shown to belong to the genus Paenibacillus and the closest phylogenetic relatives were Paenibacillus cellulosilyticus KACC 14175(T) (98.2%), Paenibacillus kobensis KACC 15273(T) (98.1%), Paenibacillus xylaniclasticus KCTC 13719(T) (96.9%), and Paenibacillus curdlanolyticus KCTC 3759(T) (96.64%). The DNA G+C content was 52.5mol%, and the predominant respiratory quinone was MK-7. The major fatty acids were iso-C15:0, iso-C16:0, and anteiso-C15:0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The results of the genotypic analysis in combination with chemotaxonomic and physiological data demonstrated that DCY89(T) represented a novel species within the genus Paenibacillus, for which we propose the name Paenibacillus ginsengiterrae. The type strain is DCY89(T) (JCM 19887(T)=KCTC 33430(T)).

Implication of HLA-G 5′ upstream regulatory region polymorphisms in idiopathic recurrent spontaneous abortions

The effect of HLA-G 5′-upstream regulatory region (URR) single nucleotide polymorphisms (SNP) in idiopathic recurrent spontaneous abortion (RSA) was evaluated. Parental genotype combination analysis and HLA-G expression at transcriptional level was evaluated for 5′URR SNP, which have shown increased risk for idiopathic RSA. If a fetus were aneuploid, attributing causation to a HLA-G 5′-URR SNP would be illogical; therefore couples with abnormal parental karyotypes and also those with abortus material that revealed chromosomal abnormalities were excluded. One hundred women who had experienced idiopathic RSA, along with their respective male partners and 100 pairs of control couples, were studied. HLA-G 5′-URR SNP were evaluated through sequencing. Quantitative polymerase chain reaction was used for HLA-G expression analysis. An increased risk for idiopathic RSA cases among women carriers of mutant genotypes of -1179G>A(rs1233335), -725C>G/T(rs915670) and -486A>C(rs114252012) SNP. The parental genotype combination analysis revealed a 3.5-fold increased risk for -1179G>A and 4.3-fold increased risk for -725C>G/T SNP among carriers of mutant parental genotypes in couples who have experienced idiopathic RSA. Down-regulation in HLA-G expression was seen at transcriptional level for -1179G>A and -725C>G/T SNPs in cases of idiopathic RSA. Transmission of a mutant allele from single carrier parents may, therefore, affect pregnancy outcome.

Associations of FASN gene polymorphisms with economical traits in Nellore cattle (Bos primigenius indicus)

The aim of this study was to identify molecular markers to be applied to marker-assisted selection. Three SNPs of the FASN gene were studied. PCR-RFLP was used for genotyping. The SNPs g.17924A>G, g.17860C>T and g.15603A>G all in the FASN gene were genotyped using the enzymes MscI, DdeI and Hae III, respectively. The animals were raised in extensive systems and belong to three lines selected for growth as part of the Selection Program of Zebu and Caracu Breeds, São Paulo, Brazil. Allele and genotype frequencies were compared between selection lines using the Genepop 3.4. Associations between polymorphisms and the traits studied were evaluated using the PROC MIXED procedure of the SAS/STAT 9.1.3. The G and C alleles were the most frequent alleles of the g.15603A>G and g.17860C>T loci, respectively. The g.17924A>G locus showed no polymorphism in the population studied. Allele and genotype frequencies differed significantly between the NeT line and the NeC and NeS lines. The g.15603A>G polymorphism tended to exert an additive effect on rump fat thickness and male yearling height. For g.17860C>T, an additive effect on male yearling height was observed. Genotype combination analysis revealed a significant effect on loin eye area. Although this study provided evidence of an association between the FASN gene and some traits, more detailed analyses are needed to obtain more efficient molecular markers.