A novel promoter polymorphism (-71C>T) in KRTHB6 gene in Indian population

We have screened the basal promoter region, of KRTHB6 gene involving CAAT and TATA boxes in randomly selected 125 individuals of Indian origin by PCR-SSCP and DNA sequencing. We observed a novel promoter polymorphism (-71C>T) which could be differentiated by using LweI restriction enzyme. The frequency of -71 C allele, allele A (Accession no AY203963), was observed to be higher ( 0.712) in comparison to -71 T allele, allele B (0.288) (Accession no. AY037552).     

Characteristics of phenotypic antibiotic resistance of Helicobacter pylori and its correlation with genotypic antibiotic resistance: A retrospective study in Ningxia

Background

Geographic differences exist in the antibiotic resistance patterns of Helicobacter pylori. Personalized treatment regimens based on local or individual resistance data are essential. We evaluated the current status of H. pylori resistance in Ningxia, analyzed resistance-related factors, and assessed the concordance of phenotypic and genotypic resistance.

Methods

Strains were isolated from the gastric mucosa of patients infected with H. pylori in Ningxia and relevant clinical information was collected. Phenotypic antibiotic susceptibility assays (Kirby–Bauer disk diffusion) and antibiotic resistance gene detection (Sanger sequencing) were performed.

Results

We isolated 1955 H. pylori strains. The resistance rates of H. pylori to amoxicillin, levofloxacin, clarithromycin, and metronidazole were 0.9%, 42.4%, 40.4%, and 94.2%, respectively. Only five tetracycline-resistant and one furazolidone-resistant strain were identified. Overall, 3.3% of the strains were sensitive to all six antibiotics. Multidrug-resistant strains accounted for 22.9%, of which less than 20% were from Wuzhong. Strains isolated from women and patients with nonulcerative disease had higher rates of resistance to levofloxacin and clarithromycin. Higher rates of resistance to metronidazole, levofloxacin, and clarithromycin were observed in the older age group than in the younger age group. The kappa coefficients of phenotypic resistance and genotypic resistance for levofloxacin and clarithromycin were 0.830 and 0.809, respectively, whereas the remaining antibiotics showed poor agreement.

Conclusion

H. pylori antibiotic resistance is severe in Ningxia. Therefore, furazolidone, amoxicillin, and tetracycline are better choices for the empirical therapy of H. pylori infection in this region. Host sex, age, and the presence of ulcerative diseases may affect antibiotic resistance of the bacteria. Personalized therapy based on genetic testing for levofloxacin and clarithromycin resistance may be a future direction for the eradication therapy of H. pylori infection in Ningxia.     

CYP1A1 and CYP2D6 polymorphism and risk of lung cancer in a North Indian population

This case–control study was conducted to examine the association between the CYP1A1 and CYP2D6 genotypes and lung cancer risk among North Indians. The estimated relative risk for lung cancer associated with the CYP1A1 Val/Val allele was 2.68, and was four-fold when cases with small cell lung cancer (SCLC) were considered alone. With regard to the metabolism of debrisoquine, no poor metabolizers were found amongst the subjects. The odds ratio of risk with the heterozygous extensive metabolizer (HEM) genotype was 1.5. However, in the presence of at least a single copy of the variant CYP1A1 MspI allele and the CYP2D6 HEM genotype, the risk was two-fold for squamous cell carcinoma (SQCC). When the CYP1A1 Val/Val and CYP2D6 HEM genotypes were taken together, the risk for SCLC was four-fold. Stratified analysis indicated an interaction between bidi smoking and variant CYP1A1 genotypes on the risk for SQCC and SCLC. Heavy smokers (Brinkman index>400) with Val/Val genotypes were at a very high risk of developing lung cancer (odds ratio 29.30, 95% confidence interval 2.42–355, p=0.008). Heavy smokers with CYP1A1 MspI (CYP1A1*1/2A or CYP1A1*2A/*2A) genotype had a seven-fold risk for SCLC compared with non-smokers. This study is the first to be carried out on a North Indian population, and, although small, suggests that CYP1A1 and CYP2D6 polymorphisms might have a role in determining the risk for lung cancer and should be investigated further.     

Interaction of Pin1 with Nek6 and characterization of their expression correlation in Chinese hepatocellular carcinoma patients

The peptidyl-prolyl isomerase Pin1 is prevalently overexpressed in human cancers and is regarded as a new diagnostic and therapeutic target. Pin1 interacts with several proteins involved in cell cycle events in a phosphorylation-dependent manner. Among them, NIMA (never in mitosis, gene A) was first identified to interact with Pin1. In this report, we found that Pin1 could interact with Nek6, one of the human NIMA-related kinases (Neks). This interaction was confirmed by GST pull-down assay, which was further confirmed by immunoprecipitation experiments, as well as immunofluorescence colocalization. We further studied Pin1 and Nek6 mRNA level in 40 pairs of hepatocellular carcinoma cases, finding significant correlations between Nek6 and Pin1 mRNA expression levels in these samples.     

A mutation of keratin 18 within the coil 1A consensus motif causes widespread keratin aggregation but cell type-restricted lethality in mice

Mutations in genes encoding epidermal keratins cause skin disorders, while those in internal epithelial keratins, such as K8 and K18, are risk factors for liver diseases. The effect of dominant mutations in K8 or K18 during embryonic development and tissue homeostasis has not been examined so far. Here we demonstrate that the dominant mutation hK18 R89C, that is highly similar to hK14 R125C, causing EBS in humans, leads to cell type-specific lethality in mice, depending on the ratio of mutant to endogenous keratins. Mice expressing hK18 R89C in the absence of endogenous K19 and K18 died at mid-gestation from defects in trophoblast giant cells, accompanied by haematomas. A single, endogenous K18 allele rescued embryonic lethality but caused aggregation of keratins in all adult internal epithelia, surprisingly without spontaneous cell fragility. Closer analysis revealed that both filaments and aggregates coexisted in the same cell, depending on the ratio of mutant to endogenous keratins. Our results demonstrate that balanced overexpression of a wild-type keratin rescued the lethal consequences of a dominant-negative mutation. This has important implications for therapy approaches of keratinopathies, suggesting that suppressing the mutant allele is not necessary in vivo.     

Identification and molecular characterization of two novel mutations in COL1A2 in two Chinese families with osteogenesis imperfecta

Osteogenesis imperfecta (OI, also known as brittle bone disease) is caused mostly by mutations in two type Ⅰ collagen genes, COL1A1 and COL1A2 encoding the pro-α1 (Ⅰ) and pro-α2 (Ⅰ) chains of type Ⅰ collagen, respectively. Two Chinese families with autosomal dominant OI were identified and characterized. Linkage analysis revealed linkage of both families to COL1A2 on chromosome 7q21.3-q22.1. Mutational analysis was carried out using direct DNA sequence analysis. Two novel missense mutations, c.3350A＞G and c.3305G＞C, were identified in exon 49 of COL1A2 in the two families, respectively. The c.3305G＞C mutation resulted in substitution of a glycine residue (G) by an alanine residue (A) at codon 1102 (p.G1102A), which was found to be mutated into serine (S), argine (R), aspartic acid (D), or valine (V) in other families. The c.3350A＞G variant may be a de novo mutation resulting in p.Y1117C. Both mutations co-segregated with OI in respective families, and were not found in 100 normal controls. The G1102 and Y1117 residues were evolutionarily highly conserved from zebrafish to humans. Mutational analysis did not identify any mutation in the COX-2 gene (a modifier gene of OI). This study identifies two novel mutations p.G1102A and p.Y1117C that cause OI, significantly expands the spectrum of COL1A2 mutations causing OI, and has a significant implication in prenatal diagnosis of OI.     

Localization of glucose-6-phosphatase and fructose-1-6-diphosphaiase in subcellular fractions from different regions of the rat brain

Two key enzymes of gluconeogenesis, glucose-6-phosphatase and fructosp-1-6-diphosphatase, were present in the cerebral hemispheres, the cerebellum and the brain stem of the rat brain. Significant activities of these-enzymes were associated with the particulate fraction.     

Mitochondrial ND6 T14502C variant may modulate the phenotypic expression of LHON-associated G11778A mutation in four Chinese families

We report here the clinical, genetic, and molecular evaluations of four Han Chinese families with Leber’s hereditary optic neuropathy. Thirty-one (20 males/11 females) of 83 matrilineal relatives in these families exhibited the variable severity and age-at-onset in visual impairment. The average age-of-onset of vision loss was 22 years old. Strikingly, these penetrances of visual impairment in these Chinese families were higher than those in other 11 Chinese pedigrees carrying the only ND4 G11778A mutation. Molecular analysis identified the known G11778A mutation and distinct sets of variants belonging to the Asian haplogroups M10a and M7c2. Of these, the T14502C mutation caused the substitution of a highly conserved isoleucine for valine at position 58 in ND6. This mutation has been associated with LHON in other Chinese families with very low penetrance of LHON. Thus, the deficient activities of complex I, caused by G11778A mutation, would be worsened by the T14502C mutation in these four Chinese families. As a result, mitochondrial dysfunctions would lead to the high penetrance and expressivity of visual loss in these Chinese families carrying both G11778A and T14502C mutations than other 11 Chinese families carrying only G11778A mutation. These data suggested that the T14502C variant may modulate the phenotypic manifestation of the G11778A mutation in these Chinese pedigrees.     

How many differentially expressed genes: A perspective from the comparison of genotypic and phenotypic distances

Identifying differentially expressed genes is critical in microarray data analysis. Many methods have been developed by combining p-value, fold-change, and various statistical models to determine these genes. When using these methods, it is necessary to set up various pre-determined cutoff values. However, many of these cutoff values are somewhat arbitrary and may not have clear connections to biology. In this study, a genetic distance method based on gene expression level was developed to analyze eight sets of microarray data extracted from the GEO database. Since the genes used in distance calculation have been ranked by fold-change, the genetic distance becomes more stable when adding more genes in the calculation, indicating there is an optimal set of genes which are sufficient to characterize the stable difference between samples. This set of genes is differentially expressed genes representing both the genotypic and phenotypic differences between samples.     

Responses to selection on genotypic or phenotypic values in the presence of genes with major effects

Summary Average genotypic responses were compared after selection for genotypic values and for phenotypic values on the basis of single-gene models and multigene models in simulated livestock populations. Single-gene models dealt with single gene control of the genetic differences between animals, while multigene models considered a collection of genes with various magnitudes of effects on a trait. In each case, selection lasted through discrete generations until the fixation of the gene frequencies occurred. Generations to reach fixation were used to compare various models, and the two criteria for selection, for their efficiency in selection. Implications of using these models versus using infinitesimal models for selection in practice are presented.     

De novo origin of new genes with introns in Plasmodium vivax

The origin of new genes is critical for organisms adapting to new niches. Here, we present evidence for a recent de novo origin of at least 13 protein-coding genes in the genome of Plasmodium vivax. Although recently de novo originated genes have often been suggested to be initially intronless, five of the genes identified in our analysis contain introns in their coding regions. Further investigations revealed that these introns likely evolved from previously intergenic regions together with the coding sequences. We discuss the potential mechanisms for intron formation in these genes and propose that intronization be considered in the formation of de novo originated genes.     

CYP2D6 and CYP1A1 mutations in the Turkish population

Drugs and carcinogens are substrates of a group of metabolic enzymes including cytochrome p450 enzymes and gluthatione S-transferases. Many of the genes encoding these enzymes exhibit functional polymorphisms that contribute individual cancer susceptibility and drug response. Molecular studies based on these polymorphic enzymes also explain the aetiology of cancer and therapeutic management in clinics. We analysed the cytochrome p4501A1 (CYP1A1) and 2D6 (CYP2D6) variant genotype and allele frequencies by PCR-RFLP in Turkish individuals (n=140). The frequency of the CYP1A1*2A mutant allele was found to be 15.4%, and the CYP2D6*3 and *4 mutant allele (poor metabolizer) frequencies were 2.5% and 13.9%, respectively. This study presents the first results of CYP1A1 and CYP2D6 mutant allele distributions in the Turkish population and these data provide an understanding of epidemiological studies that correlate therapeutic approaches and aetiology of several types of malignancy in Turkish patients.     

Identification of three novel mutations in the COL2A1 gene in four unrelated Chinese families with spondyloepiphyseal dysplasia congenita

Introduction

Spondyloepiphyseal dysplasia congenita (SEDC) is an autosomal dominant skeletal dysplasia characterized by short stature, abnormal epiphyses, and flattened vertebral bodies. The condition occurs through a mutation in the COL2A1 gene that encodes the type II procollagen alpha1 chain (proalpha1 (II)).

Method and Results

We investigated nine affected individuals from four unrelated Chinese families with SEDC. We screened for COL2A1 gene mutations, and identified found four missense mutations (G447A, G456A, R789C and G1152D). The G447A, G456A and G1152D mutations are novel and the R789C mutation has been reported previously in several other studies with a strikingly similar phenotype.

Conclusions

Our study extends the mutation spectrum of SEDC and is helpful in early molecular diagnoses of SEDC.     

Spontaneous and induced activation of genes affecting the phenotypic expression of glucose 6-phosphate dehydrogenase in Daphnia pulex

Summary Evidence has previously been presented on the occurrence spontaneous variations in the electrophoretic mobility (EM) of glucose-6-phosphate dehydrogenase (G6PD E.C. 1.1.1.49) in laboratory clones of parthenogenetically reproducing Daphnia (Ruvinsky et al. 1983). The present study is concerned with a natural population of Daphnia living under the extreme conditions of shallow, dessicating pond. The number of individuals having the slow (S) variant of the EM of G6PD increased sharply during their 1.5 month life span. This increase is suggested to result from alternational variability related to activation of latent genetic material.     

Differential expression of insulin genes 1 and 2 in MIN6 cells and pseudoislets

There is some evidence that the two rodent insulin genes are differentially regulated in mice, although there is no satisfactory consensus on the relative levels and patterns of expression for the two genes. Using the mouse insulinoma cell line MIN6, we have demonstrated by quantitative RT-PCR, differential patterns of expression for the two genes. In mouse islets and early passage MIN6 cells, expression of ins 1 and ins 2 were found to be approximately equal, but levels of ins 1 mRNA diminished rapidly with continued passage. Furthermore, the ins 1 gene was found to be up-regulated in response to glucose stimulation and as a result of increased cell-cell contact, but no effect on the ins 2 gene was observed. Since the MIN6 cell line is frequently used as a beta-cell model for gene expression studies, consideration should be given to both insulin genes.     

Polymorphisms of interleukin-1 and interleukin-6 genes on the risk of ischemic stroke in a meta-analysis

Many epidemiological studies have investigated the associations between polymorphisms of interleukin-1 (IL1) and interleukin-6 (IL6) genes and risk of ischemic stroke (IS), but no conclusions are available because of conflicting results. The aim of this study was to assess the relationships by meta-analysis. The databases of Pubmed, Embase and Wangfang, updated to August 1st, 2011, were retrieved. Odds ratio (OR) and corresponding 95% confidence interval (95% CI) as effect size were calculated by a fixed- or random-effect model. In total, three case-control studies for IL1α-889C/T, eight studies for IL1β-511C/T, eight studies for IL1-Ra and seven studies for IL6-147G/C were included in this meta-analysis. Combined analysis indicated that IL1β-511C/T polymorphism was not overall associated with risk of IS [OR (95% CI)=1.22 (0.85-1.87) for TT vs. CC]. However, when subgroup analyses for countries were conducted, the results indicated that T allele was associated with increased risk of IS for Polish and associated with a trend of increased risk of IS for Chinese although it did not reach statistical significance [TT vs. CC: OR (95% CI)=1.97 (1.22-3.17) for Polish and 1.40 (0.99-1.99) for Chinese]. In addition, overall and subgroup analyses indicated that IL1α-889C/T, IL1-Ra and IL6-147G/C polymorphisms were also not associated with risk of IS [OR (95% CI)=1.21 (0.86-1.70) for TT vs. CC of IL1α-889C/T, 1.22 (0.85-1.75) for RN2/RN2 vs. RN1/RN1 for IL1-Ra and 1.09 (0.84-1.40) for G carriers vs. C carriers for IL6-147G/C]. This study inferred that IL1β-511C/T polymorphism might be moderately associated with increased risk of IS, but no sufficient evidence was available to support any associations between IL1-Ra and IL6-147G/C polymorphisms and IS. We could not draw a conclusion between IL1α-889C/T polymorphism and risk of IS based on the limited data, and further large sample-sized studies were required.     

Selection of human immunodeficiency virus type 1 variants with an insertion mutation in the p6(gag) and p6(pol) genes under highly active antiretroviral therapy

We detected several types of human immunodeficiency virus type 1 (HIV-1) variants with an insertion mutation in the p6(gag)and p6(pol) genes in eight of twenty-two (36.4%) patients who possessed drug-resistant viruses under highly active antiretroviral therapy (HAART). It was characteristic that a conserved proline-rich motif "PTAPP" in the N-terminus of p6(gag) protein was completely or partially duplicated in all cases. Five among the eight cases were retrospectively investigated in terms of the occurrence of dynamic change in the gag gene between the inserted and wild-type HIV-1 in the course of HAART. The longitudinal analysis revealed the following: 1) The inserted-type viruses were selected over the wild-type during HAART in three cases in which the both types coexisted in the beginning of the therapy. 2) In two cases in which the inserted-type HIV-1 alone was detected before the beginning of HAART, the inserted-type HIV-1 alone was continuously detected during the therapy. The inserted-type HIV-1 was also detected in four of thirty-nine (10.3%) therapy-naive patients. However, the frequency of inserted-type HIV-1 detection in the HAART-receiving patients is significantly higher than that in the therapy-naive patients (P = 0.02). These results suggest that this type of insertion mutation is a polymorphism of the p6(gag) and p6(pol) genes, however, it consequently gave an advantage on proliferation and/or survival of the HIV-1 variant under the presence of antiretroviral drugs.