Genetics and molecular research: GMR

Online ISSN: 1676-5680
Publications
Article
Numerous studies have evaluated the association between human leukocyte antigen (HLA) Cw*0602 polymorphism and psoriasis risk. However, the results have been inconsistent. We made a meta-analysis of the association between HLA-Cw*0602 polymorphism and psoriasis risk. Eighteen studies were retrieved, reporting a total of 3419 psoriasis patients and 3297 healthy controls. The associations between HLA-Cw*0602 polymorphism and psoriasis risk were estimated by pooled odds ratio (OR) and 95% confidence interval (95%CI). We found significant associations between HLA-Cw*0602 polymorphism and psoriasis risk in the comparisons of positive versus negative alleles (OR = 4.55, 95%CI = 3.65-5.67, P < 0.00001); positive homozygote versus negative homozygote combined with heterozygote (OR = 14.00, 95%CI = 8.47-23.15, P < 0.00001); positive homozygote combined with heterozygote versus negative homozygote (OR = 5.11, 95%CI = 3.86-6.76, P < 0.00001); positive homozygote versus negative homozygote (OR = 23.03, 95%CI = 13.95-38.00, P < 0.00001), and positive homozygote versus heterozygote (OR = 4.21, 95%CI = 2.35- 7.00, P < 0.00001). In conclusion, the positive allele of HLA-Cw*0602 polymorphism appears to be a risk factor for psoriasis.
 
Article
Plant β-1,3-glucanases are commonly involved in disease resistance. This report describes the cloning and genetic transformation of a β-1,3-glucanase gene from peanut. The gene was isolated from both the genomic DNA and cDNA of peanut variety Huayu20 by polymerase chain reaction (PCR) and reverse transcription PCR (RT-PCR), respectively. The DNA sequence contained 1471 bp including two exons and one intron, and the coding sequence contained 1047 bp that coded for a 348-amino acid protein with a calculated molecular weight of 38.8 kDa. The sequence was registered in NCBI (GenBank accession No. JQ801335) and was designated as Ah-Glu. As determined by BLAST analysis, the Ah-Glu protein has 42-90% homology with proteins from Oryza sativa (BAC83070.1), Zea mays (NP_001149308), Arabidopsis thaliana (NP_200470.1), Medicago sativa (ABD91577.1), and Glycine max (XP_003530515.1). The over-expression vector pCAMBIA1301-Glu containing Ah-Glu was constructed, confirmed by PCR and restriction enzyme digestion, and transformed into peanut variety Huayu22 by Agrobacterium EHA105-mediated transformation. The putative transformed plants (T0) were confirmed by PCR amplification. RT-PCR analysis and β-glucuronidase (GUS) staining showed that the transferred Ah-Glu was expressed as mRNA and protein. In a laboratory test, the transgenic plants were found to be more resistant to the fungal pathogen Cercospora personata than the non-transgenic plants were.
 
Article
In previous studies, we first isolated one different protein β-1,3-glucanase using two-dimensional electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry from normal wheat (Triticum aestivum L.) and chemical hybridization agent-induced male sterility (CIMS) wheat. In this experiment, β-1,3-glucanase activity and the expression of a callose deposition-related gene, UDP-glucose phosphorylase (UGPase), were determinate in normal, CIMS, and genetic male sterility (GS) wheat. β-1,3-glucanase activity was significantly different between the fertile and sterile lines during callose synthesis and degradation, but there was no difference between CIMS and GS wheat. The UGPase gene of callose deposition was highly expressed in the meiophase and sharply decreased in the tetrad stage. However, the expression of the UGPase gene was significantly different between the fertile and sterile lines. These data indicated that β-1,3-glucanase activity and the expression of the UGPase gene play important roles in the male sterility of wheat. Consequently, pollen mother cells (PMCs) might degenerate at the early meiosis stage, and differences in UGPase gene expression and β-1,3-glucanase activity might eventually result in complete pollen collapse. In addition, the critical period of anther abortion might be the meiosis stage to the tetrad stage rather than what we previously thought, the mononuclear period.
 
PbFKS 3' intron region analysis. A. Agarose gel analysis of PCR products of total DNA of Paracoccidioides brasiliensis isolates Pb 01 and Pb 4940 with primers S2 and ATS2 corresponding to 3' region of FKS gene. The arrow indicates the amplified product. B. Southern blot analysis. The gel was transferred to the nylon membrane and hybridized to the 3'PbFKS1 P2 radiolabeled probe. The arrow indicates the hybridization product. C. Agarose gel analysis of PCR products of total DNA de P. brasiliensis isolates Pb 8515, Pb 8311, Pb 8334, Pb 4268, Pb 1668, and Pb E with primers S2 and ATS2 corresponding to 3' region of FKS gene. D. Comparative analysis of the nucleotide sequences of the 3' region from the genomic fragments of PbFKS1 and PbFKS4940. Primers used in the PCR are marked by arrows; 5' GT and 3' AG splicing sites are underlined; the putative lariat sequence is boxed; intron is in bold italics, and substituted nucleotides are in bold. The sequence alignment was performed by using the CLUSTAL X program. E. Comparative analysis between the predicted amino acid sequences of the 3' region of PbFks1p and PbFks4940p. The substituted amino acids are shown in bold. The alignment was performed by using the CLUSTAL X program.
Expression analysis of PbFKS in the Pb 01 and Pb 4940 isolates. A. Gel analysis of RT-PCR products obtained by using primers S1, ATS1 and ATS3 corresponding to 5' region of the gene PbFKS. PCR control with Pb 01 DNA (lane 1); RT-PCR of Pb 01 (lane 2); RT-PCR of Pb 4940 (lane 3); control reaction without RT for PbFKS1 (lane 4); control reaction without RT for PbFKS4940 (lane 5); control reaction without RNA and RT (lane 6). The arrows indicate the amplified products. B. Southern blot analysis. The gel was transferred to the nylon membrane and hybridized to the PbFKS1 P1 radiolabeled probe. The arrows indicate the hybridization product. C. Comparative analysis of the nucleotide sequences of the 5' region from PbFKS transcripts. Primers used in the PCR are marked by arrows. The sequence alignment was performed by using the CLUSTAL X program. 
Article
The evolutionary origin and significance of spliceosomal introns have been the subject of many investigations. Two theories, "introns-early" theory and "introns-late" theory, have been proposed to explain the evolution of introns in eukaryotic genes. Intron position is generally conserved in paralogue and orthologue genes. Some introns occur at similar but not necessarily identical positions in homologous genes, which were separated by great evolutionary distances. This event can be explained by insertion, loss or movement of the intron over short distances. Intron loss and gain events are unique in evolution and can be useful as markers for phylogenetic analyses. The insertion of introns at an identical position suggests a common ancestor gene. Here we analyzed, using PCR and RT-PCR, the structure of the 1,3-beta-glucan synthase gene (FKS) in several clinical isolates of Paracoccidioides brasiliensis (Pb): isolates Pb 01, Pb 4940, Pb 8515, Pb 8311, Pb 8334, Pb 4268, Pb 1668, and Pb E. Our results showed that seven of the isolates examined showed identical structures concerning the position of introns in PbFKS1. PbFKS4940 showed the intron described at the 3' end and had lost that one at the 5' end. The presence of the PbFKS4940 transcript suggests that it could be a functional gene. These data suggest a divergent evolution for introns with regard to the 1,3-beta-glucan synthase gene in P. brasiliensis isolates.
 
Article
In this study, the phenotypic identification and molecular mechanism of one case of an A2B subtype pedigree was investigated. ABO blood groupings were identified by serological methods and sequence amplification was performed by polymerase chain reaction (PCR) using TA cloning and DNA sequencing analysis to identify the pedigree and the ABO gene haploid of the proband. There were both A and B antigens on the proband's red blood cells, and anti-A1 antibodies were found in the serum. Direct sequencing of the 6th and 7th exons of the ABO gene showed the A208/B101 genotype, and haploid determination revealed the A208 and B101 alleles. Compared with the A102 allele sequence, the A208 allele was mutated at the 539 G>C site. Pedigree analysis showed that the ABO blood phenotypes of the proband's father, mother, husband, and daughter were A2, B, AB, and A2B, respectively, and their genotypes were A208/O02, B101/B101, A102/B101, and A208/B101, respectively. The father of the proband had anti-A1 antibodies and the A208 allele of the proband was inherited from her father, which can be passed on to her daughter. The α-1, 3-N-acetylgalactose aminotransferase gene 539G>C mutation resulted in A2B phenotype generation, and individual serum contained the anti-A1 antibody.
 
Article
One of the critical enzymes involved in vitamin E biosynthesis in plants is 2-methyl-6-phytyl-1, 4-benzoquinol methyltransferase (MPBQ MT). Full-length VTE3 cDNA (designated rVTE3-1 and rVTE3-2) encoding MPBQ MT and the full-length DNA of VTE3 (designated gVTE3-1 and gVTE3-2) were isolated from cultivated peanuts (Arachis hypogaea). The full-length DNA of VTE3 (designated gVTE3-A and gVTE3-B) was isolated from the wild groundnut species A. duranensis (A-genome) and A. ipaënsis (B-genome), and polymorphism analysis of VTE3 was performed. The results demonstrated that rVTE3-1 and rVTE3-2 both have a DNA sequence that is 1059 bp-long and encodes 351 amino acids; the homology of the 2 amino acid sequences was 98.6%. The gVTE3-1 of cultivated Fenghua 2 peanut samples was 2710 bp-long, with 3 introns located at 44-163, 772-1295, and 1603-2437 bp, and the Fenghua 2 gVTE3-2 was 2706 bp-long, with 3 introns located at 44-169, 778-1291, and 1599-2433 bp. The homology for gVTE3-1 and gVTE3-2 across 13 cultivated peanut samples was 99.9 and 100%, respectively. gVTE3- 1 and gVTE3-2 were from A-genome and B-genome, respectively, with 96.6% homology between the 2 sequences. The present study demonstrated that abundant polymorphisms were present in the VTE3 genes from different genomes. Additionally, polymorphisms were observed in the gVTE3-1 alleles of the 13 cultivars and wild A. duranensis species but not in the gVTE3-2 alleles of the 13 cultivars and wild A. ipaënsis species.
 
Article
Many QTLs for fatness traits have been mapped on pig chromosome 7q1.1-1.4 in various pig resource populations. Eight novel markers, including seven SNPs and one insertion or deletion within BTNL1, COL21A1, PPARD, GLP1R, MDFI, GNMT, ABCC10, and PLA2G7 genes, as well as two previously reported SNPs in SLC39A7 and HMGA1 genes, were genotyped in Large White and Meishan pig breeds. Except for two SNPs in HMGA1 and ABCC10 genes, allele frequencies of the other eight markers are highly significant different between Chinese indigenous Meishan breeds and Large White pig breeds. Eight polymorphic sites were then used for linkage and QTL mapping to refine the fatness QTL in a Large White × Meishan F(2) resource population. Five chromosome-wise significant QTLs were detected, of which the QTLs for leaf fat weight, backfat thickness at 6-7th rib and rump, and mean backfat thickness were narrowed to the interval between PPARD and GLP1R genes and the QTL for backfat thickness at thorax-waist between GNMT and PLA2G7 genes on SSC7p1.1-q1.4.
 
Alignment of variant surface glycoprotein (VSG) LiTat 1.5 of T. b. gambiense with VSG Kinu 1 of T. b. brucei . The amino acid sequence of LiTat 1.5 was deduced from its cDNA sequence (GenBank ID: HQ662603). The amino acid residues are numbered starting with the N-terminal end of the mature protein as determined by Edman degradation. The result of the Edman degradation is underlined. The amino acid sequence of VSG LiTat 1.5 is aligned with the sequence of Kinu 1 (Genbank ID: AJ937313.1). The signal sequence is indicated in gray. Cysteines are gray and underlined, and their position in the N-terminal domain of the mature protein sequence of VSG LiTat 1.5 is numbered. The domain boundary between the nominally determined mature N- and C-terminal domains is in italics. The C-terminal hydrophobic sequence is in bold italics. The C-terminal residue is bold and underlined. Identical residues are marked with an asterisk under the sequence. Colons indicate strongly conserved substitutions (side chains with similar biochemical properties, scoring >0.5 in the Gonnet PAM 250 matrix). Periods indicate weakly conserved substitutions (scoring ≤0.5 in the Gonnet PAM 250 matrix). 
Cysteine pattern of variant surface glycoprotein N-terminal domain types. Cysteine positions are indicated as vertical bars. The scale bar (number of residues) is shown below the figure. A = N-terminal domain type A; g = group; s = subgroup. Figure adapted from Marcello and Barry (2007). 
Article
At present, all available diagnostic antibody detection tests for Trypanosoma brucei gambiense human African trypanosomiasis are based on predominant variant surface glycoproteins (VSGs), such as VSG LiTat 1.5. During investigations aiming at replacement of the native VSGs by recombinant proteins or synthetic peptides, the sequence of VSG LiTat 1.5 was derived from cDNA and direct N-terminal amino acid sequencing. Characterization of the VSG based on cysteine distribution in the amino acid sequence revealed an unusual cysteine pattern identical to that of VSG Kinu 1 of T. b. brucei. Even though both VSGs lack the third of four conserved cysteines typical for type A N-terminal domains, they can be classified as type A.
 
Article
In this study, a total of 1047 insertion-deletion (InDel) primer pairs distributed across the rice genome were developed and experimentally validated. The primer pairs were designed based on the InDel length polymorphisms between 93-11 (Oryza sativa ssp indica cv.) and Nipponbare (Oryza sativa ssp japonica cv.), aiming for utilization between indica and japonica rice, or between other inter-subspecific rice cultivars. The 1047 primer pairs were dispersed across all 12 of the rice chromosomes, with one InDel marker found every 371.3 kb on average. The InDel length of the markers varied from 3 to 39 bp: 88.2% of the markers contained 6 to 25 bp, only 6.2% of markers were ≤5 bp, and 5.6% were ≥26 bp. Six hundred and twenty-three (59.5%) of the 1047 InDel markers were shown to amplify well and were polymorphic between Taichung65 and IR8, and 476 (45.5%) markers were polymorphic between Lemont and Yangdao4, while 398 (38.0%) were polymorphic in both combinations. These results demonstrated that the polymerase chain reaction-based InDel markers developed in this study could be of immediate use for rice genetic studies and breeding programs.
 
Article
TNF 308 gene polymorphism and IL-10 polymorphism provided evidence in diagnosing some types of cancer. We aimed to explore the relation of gene polymorphism with gastric cancer. A total of 360 cases of gastric cancer patients were included in the study. The genotypes GG, GA, and AA of the interleukin-10-1082 gene (IL-10-1082) and the tumor necrosis factor-alpha gene (TNF-α) 308 polymorphism were examined by chromogenic detection. Three hundred healthy individuals' gene as control group were also examined. The GA 308 genotype of TNF-αdiffered significantly between the control group and the gastric cancer group (X(2) = 9.32, P < 0.05). Genotype frequencies of A/A (17.2%), A/G (26.2%), and G/G (9.1%) of the IL-10-1082 gene polymorphism in the gastric cancer group differed significantly compared to those of the control group (X(2) = 20.32, P < 0.05). The IL-10-1082 gene and the GA 308 genotype of the TNF-αgene were found to be susceptibility genes for gastric cancer.
 
Differential expression of the 11β-HSD1 gene in epicardial adipose and ascending aorta tissues of metabolic syndrome (MS) and control groups. Values are reported as means ± standard deviation. *Statistical significance was taken at P < 0.05. Comparisons were made between MS and control groups. 
Correlations between 11β-HSD-1 expression levels in epicardial adipose tissue (EA) and ascending aorta tissue (AA) with obesity parameters [waist-to-hip ratio, body mass index (BMI) and high-density lipoprotein (HDL) levels]. A. 11β-HSD-1 expression levels in EA tissue were positively correlated with waist-to-hip ratio (r = 0.695; P = 0.004). B. A negative correlation was identified between 11β-HSD-1 expression levels in EA tissue and HDL levels (r = -0.561; P = 0.03). C. Correlation between 11β-HSD-1 expression levels in AA tissue and BMI (r = 0.756; P = 0.001). 
Article
11β-hydroxysteroid dehydrogenase type 1 (11β-HSD-1) activity and mRNA levels are increased in visceral and subcutaneous adipose tissues of metabolic syndrome subjects. We analyzed 11β-HSD-1 expression in human epicardial adipose (EA) and ascending aorta (AA) tissues of metabolic syndrome patients and examined their contribution to the development of coronary atherosclerosis. The 11β-HSD-1 expression was evaluated by qRT-PCR in EA and AA tissues of 20 metabolic syndrome patients with coronary artery disease (metabolic syndrome group) and 10 non-metabolic syndrome patients without coronary artery disease (controls). 11β-HSD-1 expression was increased in EA and AA tissues of the metabolic syndrome group (4.1- and 5.5-fold, respectively). A significant positive correlation was found between 11β-HSD-1 expression in EA tissue and waist hip ratio and 11β-HSD-1 expression in AA tissue and body mass index, while a negative correlation was found between 11β-HSD-1 expression in EA tissue and HDL. Expression of CD68, a macrophage marker, was significantly increased in both tissues of the metabolic syndrome group; it was 2-fold higher in AA tissue compared to EA tissue in the metabolic syndrome group. Our findings of increased expression of 11β-HSD-1 and CD68 in AA tissue of the metabolic syndrome group lead us to suggest that they contribute to coronary atherosclerosis in metabolic syndrome. This positive correlation between obesity markers and 11β-HSD-1 in AA and EA tissues strengthens the evidence that 11β-HSD-1 has a role in metabolic syndrome. To the best of our knowledge, this is the first report showing 11β-HSD-1 and CD68 expression in AA tissue of metabolic syndrome patients. We suggest that there is tissue-specific expression of 11β-HSD-1 in metabolic syndrome and associated cardiovascular disorders.
 
Cluster analysis of 11 cotton accessions based on Nei's similarity matrices.  
Article
The genetic distance of 11 cotton genotypes varying in heat tolerance was studied using RAPD markers. Fifty-three random decamer primers were used for the estimation of genetic distance. Among the 53 RAPD primers, which were custom synthesized by GeneLink Inc., UK, 32 were polymorphic and 21 were monomorphic. The 32 polymorphic primers produced 273 fragments, with a mean of 8.3 fragments per primer. The number of polymorphic bands produced in the 11 cotton accessions ranged from 1 to 31. Primer GLC-20 produced 31 polymorphic bands, while two primers, GLB-5 and GLC-12, produced one polymorphic band each. A range of 88.89 to 42.48% genetic similarity was observed among the 11 cotton accessions. The highest genetic similarity was observed between FH-945 and BH-160 (88.89%), whereas the lowest value was found between NIAB-801/2 and FH-945 (42.48%). Unique amplification profiles were produced by most of the cultivars; the differences were sufficient to distinguish them from other genotypes. This confirms the efficacy of RAPD markers for the identification of plant genotypes. An accumulative analysis of amplified products generated by RAPDs was sufficient to assess the genetic diversity among the genotypes. This information should be helpful for formulating breeding and genome mapping programs.
 
Article
KCNE1, a membrane protein that spans the membrane once is responsible for modulating potassium channel functions and plays an important role in the etiology of arrhythmia. Emerging evidence indicates that a common polymorphism (112G>A; rs1805127 G>A) in the KCNE1 gene contributes to atrial fibrillation (AF) risk; however, these studies showed inconclusive results. In this meta-analysis, we derived a more precise estimation of the association between the KCNE1 112G>A polymorphism and AF risk. The following databases were searched: Web of Science (1945-2013), the Cochrane Library Database (Issue 12, 2013), PubMed (1966-2013), EMBASE (1980-2013), CINAHL (1982-2013), and the Chinese Biomedical Database (1982-2013). The crude odds ratios with their 95% confidence intervals were calculated. Nine case-control studies were included, with a total of 1792 AF patients and 1924 healthy controls. The meta-analysis results indicated that the KCNE1 112G variant is associated with an increased risk of AF. Further subgroup analysis based on ethnicity revealed significant associations between the KCNE1 112G variant and an increased risk of AF among both Asians and Caucasians. No publication bias was detected in this meta-analysis. In conclusion, our results indicate that the KCNE1 112G polymorphism may be a risk factor for AF. KCNE1 112G>A may be useful as a biomarker for predicting the development of AF.
 
Agarose gel (1%) showing PCR fragments of CD14 polymorphisms. Lane M = 100-bp marker; lane C = control. A. PCR fragments of CD14-159. B. PCR fragments of CD14-1145. 
DNA sequences of the CD14 promoter of G(-1145)A and C(-159)T. C-159T: A. genotype C/C; B. genotype C/T; C. genotype T/T. G-1145A: A. genotype G/G; B. genotype G/A; C. genotype A/A. 
Allele frequencies for the CD14 SNPs in cases and controls.
Article
Although the role of CD14 in mediating signals from Toll-like receptors to recognize Mycobacterium tuberculosis is known, how polymorphisms in this gene affect the susceptibility to develop tuberculosis are still not clear. We examined whether single nucleotide polymorphisms at positions -1145 and -159 in the promoter region of the CD14 gene are associated with tuberculosis in a Chinese Han population in a case-control study of 432 Chinese patients with tuberculosis and 404 ethnically matched healthy controls. Genotyping was performed to identify polymorphisms of the CD14 gene by PCR-DNA sequencing. Both the frequency of allele T in the C(-159)T polymorphism (odds ratio (OR) = 1.4; 95% confidence interval (95%CI) = 1.148-1.708) and allele G in the G(-1145)A polymorphism (OR = 1.512; 95%CI = 1.236- 1.849) were significantly more frequent in cases than in controls. The frequencies of genotypes CC and CT in the C(-159)T polymorphism, as well as the frequencies of genotypes AA and AG, were lower in cases than in controls. Based on our results, we conclude that G(-1145)A and C(-159)T polymorphisms of CD14 are associated with decreased risk for the development of tuberculosis in the Chinese Han population.
 
Article
Vascular endothelial growth factor (VEGF) regulates endothelial cell proliferation, migration and differentiation. VEGF plays a critical role in angiogenesis during placenta formation. We investigated whether VEGF gene polymorphisms are associated with recurrent pregnancy loss. Thirty-eight women with recurrent pregnancy loss and 30 control women with live-born children were recruited from 2010 to 2011 in the region of Bursa, Turkey. VEGF gene polymorphisms were assessed with PCR-RFLP analysis of DNA samples obtained from leukocytes. DNA fragments were investigated by using appropriate primers. SNP scanning was performed using MnII, BgIII, BshI2361, Hsp92II restriction enzymes for 1154 G/A, 2578 C/A, 460 C/T, and 936 C/T polymorphisms, respectively. The frequencies of 2578 C/A, 460 C/T, 936 C/T polymorphisms were not significantly different between the controls and women with recurrent pregnancy loss. However, the prevalence of the 1154 G/A polymorphism A/A genotype was significantly higher in the recurrent pregnancy loss group (23.7 vs 3.4%). One of the four common polymorphisms of the VEGF gene was found to be more frequent in women with recurrent pregnancy loss. It is possible that disruption of VEGF function and placental angiogenesis can contribute to pregnancy loss in women with recurrent pregnancy loss.
 
Article
The regulation mechanism and significance of microRNA-122 (miRNA-122) expression are unclear. The aim of this study was to investigate the effects of DNA methylation on liver-specific miRNA-122 expression, cell proliferation, and apoptosis in hepatocellular carcinoma. Methylation of the miRNA-122 promoter region was detected through methylation sequencing. The level of miRNA-122 expression was measured using real-time quantitative polymerase chain reaction. The proliferation and apoptosis of hepatocellular cell lines were detected using flow cytometry and Cell Counting Kit-8 assays. Compared with those in human primary hepatocytes, methylation levels of the miRNA-122 promoter in the Huh7, HepG2, and QSG-7701 cell lines were significantly increased (P = 0.000). Similarly, levels of miRNA-122 expression in these cell lines significantly decreased (P = 0.007). After treatment with 5-aza-2-deoxycytidine, the Huh7 and HepG2 cell lines displayed a significantly lower degree of methylation (P = 0.038 and 0.025), and the levels of miRNA-122 expression were significantly higher (P = 0.008 and 0.003) than those in the blank group. Compared with the blank group, apoptosis of Huh7 and HepG2 cells was significantly increased (P = 0.001 and 0.027). We concluded that the expression of miRNA-122 is regulated by DNA methylation and correlated with apoptosis of liver cancer cells. Methylation regulation of miRNA-122 expression might be involved in the development of hepatocellular carcinoma.
 
Genotypic distribution and frequencies in 3435 C/T and 1236 C/T polymorphisms of ABCB1 in preand postmenopausal women. 
Analysis of ABCB1 3435 C/T and 1236 C/T polymorphisms in pre-and postmenopausal women. 
Article
MDR1, which is encoded by the ABCB1 gene, is involved in multidrug resistance (hydrophobic), as well as the elimination of xenotoxic agents. The association between ABCB1 gene polymorphisms and breast cancer risk in different populations has been described previously; however, the results have been inconclusive. In this study, we examined the association between polymorphisms 3435 C/T and 1236 C/T in the ABCB1 gene and breast cancer development in Mexican women according to their menopausal status and molecular classification. Molecular subtypes as well as allele and genotype frequencies were analyzed. A total of 248 women with initial breast cancer diagnosis and 180 ethnically matched, healthy, unrelated individuals were enrolled. Polymerase chain reaction-restriction fragment length polymorphism was performed to detect polymorphisms 3435 C/T and 1236 C/T in the ABCB1 gene. Premenopausal T allele carriers of the 3435 C/T polymorphism showed a 2-fold increased risk of breast cancer with respect to the reference and postmenopausal groups, as well as triple-negative expression regarding the luminal A/B molecular subrogated subtypes. In contrast, the CT genotype of the 1236 polymorphism was a protective factor against breast cancer. We conclude that the T allele carrier of the 3435 C/T polymorphism in the ABCB1 gene in combination with an estrogen receptor-negative status may be an important risk factor for breast cancer development in premenopausal women.
 
Article
Over the past decade, an increasing number of studies have demonstrated correlations between host genetics and susceptibility to diseases. However, few studies have investigated the effects of host genetics on the occurrence of opportunistic infections among human immunodeficiency virus (HIV) and acquired immunodeficiency syndrome (AIDS) patients. In the present study, the frequency of the interleukin (IL)-7Rα+1237 A/G single nucleotide polymorphisms was determined in relation to opportunistic infection occurrence among HIV and AIDS patients in the Vhembe District. Demographic, clinical, and socioeconomic status data were collected from patients using a structured questionnaire. Genomic DNA was extracted from mouthwash samples using the QIAmp Blood Mini Kit. Genotyping of the IL-7Rα+1237 gene was conducted using a sequence-specific polymerase chain reaction method. We found that the IL-7Rα+1237 genotype distribution in our study population differed from those in European populations with a predominance of the A/G genotype. Individuals carrying the A/G genotype primarily suffered from chest pain (χ(2) = 5.016, P = 0.025), while individuals carrying the G/G genotype were protected from chest pain but had a higher prevalence of sexually transmitted disease (23 vs 16.9%); however, the difference was not statistically significant (P = 0.435). Individuals carrying the A/A genotype were more susceptible to diarrhea (32 vs 13.6%) (P = 0.034). Our data will support gene therapy and may be used to modify the course of diseases among HIV patients as well as the general population. Further studies using larger populations are needed to confirm these hypotheses.
 
Position of the CvP prophages and the Rhs (recombination hot spot) element in the Chromobacterium violaceum genome. CvP1-CvP4 = C. violaceum phages 1 to 4. 
Article
A fluid genome is a great advantage to prokaryotes, enabling quick adaptation to various types of ecological niches and to diverse environmental selective pressures. A substantial portion of these sudden changes is mediated by lateral gene transfer (LGT), through genetic recombination mechanisms, such as transformation, conjugation and transduction. The recent sequencing of several organisms has offered a new approach to the study of LGT, using comparison and analysis of nucleotide sequences dispersed throughout the genome of these species. This analysis in Choromobacterium violaceum has revealed four prophage and 12 insertion sequences, suggesting genetic exchange with several other bacterial species, including Salmonella enterica, Ralstonia and Xanthomonas. An Rhs (recombination hot spot) element (containing a vgr-like gene) was also observed, the function of which remains unknown, but it has a sequence related to species of Acinetobacter and Sphingomonas. These results support the role of LGT in the acquisition of new traits by C. violaceum.
 
Article
Telomere biology is intimately linked to the genetic/environmental etiology of cardiovascular and metabolic diseases and telomere shortening is emerging as an important biomarker disease. The relationship between subtelomeric deletions and genetic hypertension was examined. Fluorescence in situ hybridization was used to directly assess whether there is a loss or gain of subtelomere copy number. Five subjects with essential hypertension and five normotensive controls were recruited from the outpatient population of the Cardiology Department of the Afyon Kocatepe University Medical School. Fluorescence in situ hybridization was performed using 12p(Tel12) and 15q(Tel15) Cytocell subtelomeric probes on metaphase slides prepared from peripheral blood samples. No differences in subtelomeric region signals between the hypertensive and normotensive groups were found.
 
Article
A pair of new universal 12S mitochondrial rRNA gene primers was designed through multiple alignment analysis of the mitochondrial tRNA(Phe) and the 5' region of 16S mitochondrial rRNA genes of different kinds of fishes. The primers were successfully used to amplify an expected product fragment of about 1.2 kb from various marine fish species, and the amplified DNA fragment was recognized to contain the complete 12S mitochondrial rRNA and tRNA(Val) genes, as well as a partial 16S mitochondrial rRNA gene of about 146 bp in length. The primers would facilitate the study of the species discrimination, population and evolution in marine fish species.
 
Article
PCR has been extensively used for amplification of DNA sequences. We conducted a study to obtain the best amplification conditions for cytochrome b (Cyt b), cytochrome c oxidase I (COI) and 12S rRNA (12S) gene fragments of Malayan gaur mtDNA. DNA from seven Malayan gaur samples were extracted for PCR amplification. Various trials and combinations were tested to determine the best conditions of PCR mixture and profile to obtain the best PCR products for sequencing purposes. Four selected target factors for enhancing PCR, annealing temperature, concentration of primer pairs, amount of Taq polymerase, and PCR cycle duration, were optimized by keeping the amount of DNA template (50 ng/μL) and concentration of PCR buffer (1X), MgCl(2) (2.5 mM) and dNTP mixture (200 μM each) constant. All genes were successfully amplified, giving the correct fragment lengths, as assigned for both forward and reverse primers. The optimal conditions were determined to be: 0.1 μM primers for Cyt b and COI, 0.3 μM primers for 12S, 1 U Taq polymerase for all genes, 30 s of both denaturation and annealing cycles for Cyt b, 1 min of both stages for 12S and COI and annealing temperature of 58.4 ° C for Cyt b, 56.1 ° C for 12S and 51.3 ° C for COI. PCR products obtained under these conditions produced excellent DNA sequences.
 
The geographical distribution of the seven Presbytis species according to Oates et al. (1994) and adapted from Md-Zain et al. (2008). 
Neighbor joining phylogram of Cyt b based on the Kimura-2-parameter. Number above branches is the bootstrap value (1000 replications). 
Neighbor joining phylogram of 12S rRNA based on the Kimura-2-parameter. Number above branches is the bootstrap value (1000 replications). 
The maximum parsimony heuristic bootstrap tree of Cyt b . The bootstrap support values are shown above the branches of the parsimony tree. 
The maximum parsimony heuristic bootstrap tree of 12S rRNA. The bootstrap support values are shown above the branches of the parsimony tree. 
Article
Little is known about the classification and phylogenetic relationships of the leaf monkeys (Presbytis). We analyzed mitochondrial DNA sequences of cytochrome b (Cyt b) and 12S rRNA to determine the phylogenetic relationships of the genus Presbytis. Gene fragments of 388 and 371 bp of Cyt b and 12S rRNA, respectively, were sequenced from samples of Presbytis melalophos (subspecies femoralis, siamensis, robinsoni, and chrysomelas), P. rubicunda and P. hosei. The genus Trachypithecus (Cercopithecidae) was used as an outgroup. The Cyt b NJ and MP phylogeny trees showed P. m. chrysomelas to be the most primitive, followed by P. hosei, whereas 12S rRNA tree topology only indicated that these two species have close relationships with the other members of the genus. In our analysis, chrysomelas, previously classified as a subspecies of P. melalophos, was not included in either the P. m. femoralis clade or the P. m. siamensis clade. Whether or not there should be a separation at the species level remains to be clarified. The tree topologies also showed that P. m. siamensis is paraphyletic with P. m. robinsoni, and P. m. femoralis with P. rubicunda, in two different clades. Cyt b and 12S rRNA are good gene candidates for the study of phylogenetic relationships at the species level. However, the systematic relationships of some subspecies in this genus remain unclear.
 
Article
Interleukin (IL)-13 is a central mediator in allergic asthma. Our previous results have indicated that sulfatase-modifying factor 2 (SUMF2) interacts with IL-13 and inhibits its secretion. In this study, we investigated the interactions between SUMF2 subtypes and 2 types of IL-13. Wild type IL-13 (wh-IL-13) and its mutated counterpart (mh-IL-13) were analyzed and cloned into pSos yeast expression vectors. Protein was expressed in host cdc25H yeast strains. A quartet of agar growth plates was prepared for the yeast two-hybrid system, which was used to detect IL-13 and SUMF2 subtype interactions. Both yeast expression vectors, pSos/whIL-13 and pSos/whIL-13, and recombinant expression vectors for the 5 subtypes of SUMF2 (pMyr/SUMF2-Vx) were constructed. Our data showed that all of the SUMF2 subtypes bound to whIL-13 and mhIL-13 in the CytoTrap system. Five SUMF2 subtypes - SUMF2-V2, SUMF2-V3, SUMF2-V4, SUMF2-V5, and SUMF2-V7 - interacted with whIL-13 and mhIL-13. These subtypes may contribute to allergic asthma by mediating IL-13 release.
 
Article
Larimichthys polyactis is a commercially important marine fish species in southeast Asia. The population crashed due to overfishing in the 1970s, but has since recovered. We developed 13 novel polymorphic microsatellite markers in L. polyactis using 5' anchored PCR. The characteristics of these loci were estimated by analyzing a sample of 30 individuals. A total of 74 alleles were detected, with a mean of 5.7 alleles per locus. There were 2 to 12 alleles, 0.2760 to 0.8247 polymorphism information content, and 0.3214 to 1.000 observed and 0.3097 to 0.8567 expected heterozygosity per locus. The mean observed and expected heterozygosity was 0.6816 and 0.6724, respectively. Three loci deviated significantly from Hardy-Weinberg equilibrium after Bonferroni's correction, and no significant linkage disequilibrum between pairs of loci was found. This information will be useful for the analysis of population genetic diversity, and the management of this important fish resource.
 
Article
Dear Editor, In answer to the questioning of the terminology we used in our manuscript (Chen et al., 2014), ASP is a 76-amino acid (8932 Da) fragment, which is identical to C3adesArg, a cleavage product of complement C3. Cleavage of complement C3 is mediated via the alter-nate complement pathway by the interaction of C3, factor B and adipsin (Factor D, a serine protease enzyme), which generates C3a. Rapid cleavage of the C terminal arginine of C3a by carboxypeptidase N generates ASP (Hugli, 1990). Activation of this pathway is initiated through the C3b component of C3 (ASP precursor) associated with the plasma membrane. In the presence of Mg(2+), Factor B binds to the activated C3b to form a C3bB complex. This, in turn, induces a conformational change of Factor B, permitting proteolytic cleavage by adipsin. The action of adipsin on C3b-bound Factor B generates a C3bBb fragment (a C3 convertase), which in turn cleaves complement C3 into C3b and C3a (Schreiber and Muller-Eberhard, 1978; Lesavre et al., 1979). The C3b component can then be recycled back to start the process anew. The carboxy-terminal arginine of C3a is rapidly cleaved in plasma by carboxypeptidase N to form C3adesArg (ASP) (Campbell et al., 2002). ASP Generation Genes, as previously published (Cianflone et al., 1989; Sniderman and Cianflone, 1994), are the key genes involved in the conversion of complement C3 toits ASP form (aka C3adesArg); C3, factor B and adipsin are produced by adipocytes. These three genes also correlated closely with other genes and have been called the "ASP triad" (MacLaren et al., 2010). Based on previous studies, we chose the C3-related SNP to investigate the relation-ship between this C3-related gene and coronary heart disease. In previous studies, the C3 gene was also described as an ASP-related gene, an ASP generation gene and an ASP gene, while in our paper we used the term ASP gene (MacLaren et al., 2010; Farahbakhsh-Farsi et al., 2014). It may not be an accurate descriptive name, but it is not unreasonable to use such a designa-tion, as there is no unique definition of these genes, which are related to ASP generation. Nevertheless, we appreciate the careful reading of our manuscript. If there are any other questions or suggestions, with readers are welcome to contact us through the e-mail provided in our published paper.
 
Article
A ring chromosome 13 or r(13) exhibits breakage and reunion at breakage points on the long and short arms of chromosome 13, with deletions of the chromosomal segments distal to the breakage points. The r(13) chromosome accounts for approximately 20% of ring chromosomes compatible with life. We describe a female patient with mental retardation, growth retardation, microcephaly, craniofacial dysmorphy, hearing impairment, and prolonged prothrombin time. Chromosomal analysis via GTG banding of peripheral blood lymphocytes revealed a karyotype of 46,XX,r(13)(p13q34)[71]/45,XX,-13[12]/ 46,XX,dic r(13;13)(p13q34;p13q34)[9]/46,XX,-13,+mar[5]/47, XX,+r(13) (p13q34)x2[2]/46,XX[1] at the age of 6 years and 46,XX,r(13)(p13q34)[82]/45,XX,-13[14]/46,XX,dic r(13;13)(p13q34; p13q34)[2]/46,XX, -13,+mar[2]. Array comparative genomic hybridization analysis of the blood demonstrated a 4.37-Mb deletion on chromosome 13q [arr cgh 13q34q34(109,743,729-144,110,721)]. A cytogenetic study of peripheral blood revealed a rare chromosomal abnormality associated with different cell lines that included structural and numerical abnormalities of chromosome 13. This case, along with 14 previously reported cases, indicate that the smallest critical region for chromosome 13 microcephaly is 109,743,729-144,110,721.
 
Article
Dear Editor, As a scientist who works on obesity and immunity, especially the complement system, I read the paper titled "Relationship between the acylation-stimulating protein gene and coro-nary heart disease in the Xinjiang Uygur and Han populations of China" published in Genetics and Molecular Research 13 (2): 2638-2644 (2014). I was surprised when I read about the "acylation-stimulating protein (ASP) gene" and its correlation with heart disease. As the authors stated in their abstract, "ASP is identical to C3a desArg, and produced through the interaction of the precursor protein C3, Factor B, and adipsin (also known as Factor D), components of the alternative complement immune path-way, which are secreted by the adipose tissue". This is correct. This also means that there is noacylation-stimulating protein gene, as this protein is made post-transcriptionally through the interaction of Complement C3, Factor B and Factor D. The "ASP gene" is actually the gene of precursor protein C3, which is also the main component of the complement system of in-nate immunity; it is directly and strongly linked with CHD. In the paper, the polymorphism is described as only affecting ASP, which is incorrect. The concept of an ASP gene is misleading. In reality, the authors have linked a polymorphism in the C3 gene with coronary heart disease in a specific population; this polymorphism could also potentially alter ASP function. I hope my criticism is taken positively, as I only aim to correct what I believe is a genuine mistake, in order to avoid scientific inaccuracy.
 
Article
The article "ZNF797 plays an oncogenic role in gastric cancer" by D. Momenzadeh, S. Rahman Zadeh, M. Rezaei-Tavirani, A. Baradaran-Rafii, F. Ghasemvand and S. Heidari-Keshel published in Genetics and Molecular Research vol. 13 (4), pp. 8421-8427 in 2014, DOI: http://dx.doi.org/10.4238/2014.October.20.18, has been found to be substantially equal to the article "Role of SALL4 in the progression and metastasis of colorectal cancer" published in the Journal of Biomedical Science, vol. 20, p. 6 in 2013, DOI: 10.1186/1423-0127-20-6, by other authors. The corresponding author of the article published in Genetics and Molecular Research, Saeed Heidari-keshel, alerted our editorial staff about this situation and requested that the article should be retracted. After review and after contacting the authors, the editors of Genetics and Molecular Research have decided to retract the article. The authors and their institutions have been advised of this serious breach of ethics.
 
Article
The article "Absolute quantification of free tumor cells in the peripheral blood of gastric cancer patients" by N. Bayat, M.M. Mokhtari, M. Rezaei-Tavirani, A. Baradaran-Rafii, S. Rahman Zadeh, S. Heidari-Keshel and F. Ghasemvand published in Genetics and Molecular Research vol. 13 (2), pp. 4425-4432 in 2014, DOI: http://dx.doi.org/10.4238/2014.June.16.1, has been found to be substantially equal to the article "Quantitative analysis of TEM-8 and CEA tumor markers indicating free tumor cells in the peripheral blood of colorectal cancer patients". published in International Journal of Colorectal Disease vol. 26 (10), pp. 1265-1270 in 2011, DOI: 10.1007/s00384-011-1230-8, by other authors. The corresponding author of the article published in Genetics and Molecular Research, Saeed Heidari-keshel, alerted our editorial staff about this situation and requested that the article should be retracted. The results are surprisingly similar, with the number of positive patients being almost the same, for example. After review and after contacting the authors, the editors of Genetics and Molecular Research have decided to retract the article. The authors and their institutions have been advised of this serious breach of ethics.
 
Article
This paper has been retracted with the consent of the submitting author, Hui Wang because of serious plagiary issues. The same article was previously published in the African Journal of Pharmacy and Pharmacology vol. 6 (24), pp. 1746-1752 in 2012, DOI: 10.5897/AJPP12.067; the authors were Qinghua Zhou, Yun Li and Baihua Chen. The republication of this article is a serious breach of scientific ethics. After Dr. Wang was informed of this situation; he agreed that the paper should be retracted. We also contacted Dr. Wang's institution, a University Hospital in China. After we made contact, the vice director of that institution indicated that he was sorry "for the academic misconduct of our employee" and requested retraction of the article and promised that "similar things will not happen in the future".
 
Mean mitotic index and percentage of chromosomal aberrations in the negative control group (CO - ) and the solvent group (CS) and treated with beta-carotene (BC) and 131I 1 in the acute treatment of Wistar rats; 1 Results published in Düsman et al. (2011). Treatments: SIM = simultaneous; PRE = pre-treatment; POST = post-treatment. *Statistically significant result in relation to CO - (P < 0.05). # Statistically significant result in relation to CS (P < 0.025). § Statistically significant result compared to BC (P < 0.005). & Statistically significant result compared to 131I (P < 0.025). 
Rate of radiation exposure and elimination of 131I in acute treatments of Wistar rats. SIM = simultaneous; PRE = pre-treatment; POST = post-treatment. 
Percentages of mitotic index and chromosomal aberrations that were obtained from the negative control group (CO - ) and the solvent group (CS) and beta-carotene (BC) and 131I 1 treatment in the subchronic treatment of Wistar rats. 1 Results published in Düsman et al. (2011). Treatments: SIM = simultaneous; PRE = pre-treatment; POST = post-treatment; CONT = continuous. *Statistically significant result in relation to CO - (P < 0.025). # Statistically significant result in relation to CS (P < 0.025). 
Rates of radiation exposure and elimination of 131I. Radiation exposure and elimination of 131I were measured at different times during the subchronic treatments. SIM = simultaneous; PRE = pre-treatment; POST = post-treatment; CONT = continuous. 
Water consumption was measured in different groups that were sacrificed after 24 h and 5 days of 131I administration. Treatments: CO - = negative control; 131I = treated with iodine-131 1 ; SIM = simultaneous; PRE = pre-treatment; POST = post-treatment; CONT = continuous. 1 Results published in Düsman et al. (2011). *Statistically significant result in relation to CO - (P < 0.005). § Statistically significant result compared to BC (P < 0.005). & Statistically significant result in relation to 131I (P < 0.005). 
Article
Radioactive iodine-131 (131I) is used in the treatment and diagnosis of thyroid gland injuries. However, because it emits ionizing radiation, it causes harmful effects to cells. Given that beta-carotene (BC) has antioxidant and antigenotoxic properties, this study aimed to investigate its radioprotective and antimutagenic activity in relation to 131I at the dose that is used to treat hyperthyroidism using a test system of bone marrow cells from Wistar rats (Rattus norvegicus). The doses were 0.2 mL of 8 mg BC/mL corn oil and 25 μCi 131I per 100 g body weight, and they were given via gavage in acute and subchronic treatments. Treatment groups included simultaneous, pre-treatment, post-treatment, and continuous treatment types. In all antimutagenic acute treatments, BC had a significant antimutagenic/radioprotective activity in relation to 131I. In subchronic antimutagenic treatments, BC reduced the damage that was caused by the radioisotope; however, this reduction was not statistically significant because of the relatively low percentage of chromosomal abnormalities that were observed with only 131I compared to the acute treatment. These results demonstrate the radioprotective and antimutagenic activity of BC, indicating its use by the population, which inevitably is exposed to mutagenic agents, as a means of health protection.
 
Average number of micronuclei (MN) and standard deviation for the negative (CO-) and positive (DXR- doxorubicin) control groups compared to the groups exposed to 0.1 to 10 μCi of [ 131 I]. *The results are significantly different compared to the CO-. 
Average number of micronuclei (MN) and standard deviation for the negative (CO-) and positive (DXR- doxorubicin) control groups compared to groups treated with 10 μL of DMSO/mL (dimethylsulfoxide), 0.2, 1, and 2 μM of beta-carotene (BETA) and 0.025, 0.125 and 0.25 g of acerola pulp/mL (ACE). *The results are significantly different from the CO-. 
Average number of micronuclei (MN) and standard deviation for the negative control group (CO-) and groups treated with 10 μCi of 131 Iodine (I), 10 μL of DMSO/mL (dimethylsulfoxide), 0.2 μM of beta-carotene (BETA), and 0.25 g of acerola pulp/mL (ACE), with and without [ 131 I]. *The results are significantly different compared to the negative control (CO-). #The results are significantly different compared to DMSO. §The results are significantly different compared to beta-carotene. 
Article
The radioisotope iodine-131 [(131)I] can damage DNA. One way to prevent this is to increase the amount of antioxidants via dietary consumption. The goal of this study was to evaluate the radioprotective effect of fresh acerola pulp and synthetic beta-carotene in Rattus norvegicus hepatoma cells (HTC) in response to [(131)I] exposure in vitro. Cellular DNA damage was subsequently assessed using a cytokinesis block micronucleus assay. The mutagenic and cytotoxic activities of doses of [(131)I] (0.1, 0.5, 1, 5, and 10 µCi), acerola (0.025, 0.125, and 0.25 g acerola pulp/mL), and beta-carotene (0.2, 1, and 2 µM) were evaluated. Radioprotective tests were performed by simultaneous treatment with acerola (0.25 g/mL) plus [(131)I] (10 µCi) and beta-carotene (0.2 µM) plus [(131)I] (10 µCi). Acerola, beta-carotene, and low concentrations of [(131)I] did not induce micronucleus formation in HTC cells; in contrast, high concentrations of [(131)I] (10 µCi) were mutagenic and induced DNA damage. Moreover, neither acerola nor beta-carotene treatment was cytotoxic. However, acerola reduced the percentage of [(131)I]-induced damage, although beta-carotene did not show a similar effect. Thus, our results suggest that acerola diet supplementation may benefit patients who are exposed to [(131)I] during thyroid diagnostics and therapy.
 
Electropherograms and gels of the seven families showing all duplications found in this study. The arrows indicate the duplications. 
Article
In September 1987, in Goiânia, Brazil, one of the most serious radiological accidents occurred at a radiation therapy unit involving a source of cesium-137. The current study examined the occurrence of possible germline mutations at the AZF region of the exposed men and in their male offspring. Genomic DNA samples of 16 individuals were analyzed for microdeletions. All exposed individuals amplified sequence tagged sites; however, sY84 and sY86 showed a duplication in 75% (12/16) of the exposed group. Exposed families designated as B and E showed a duplication of sY84 and sY86, both in the fathers and their sons. Fathers of families A, C, D, and F did not show a duplication in the AZF region, but their sons did. The children in A and D had duplications of sY84 and sY86, while children in families C and F had a duplication exclusively of sY84. Family G showed a duplication of sY84 in all three generations from grandfather to grandson. Two human endogenous retroviral sequences (HERV) exist in the AZFa region, and non-allelic recombination between these sequences could cause chromosomal rearrangements, such as deletions or duplications, and a mutational mechanism intrinsic to non-allelic recombination could be increased by individual exposure to ionizing radiations from cesium-137. Consequently, the hotspots inside HERV mediated recombination in AZFa, and the duplication diversity was compatible with male fertility, since to date, none of the exposed individuals have demonstrated fertility disorders.
 
Amplification plot and standard curve from assay using an endogenous gene KRAS using 4 standards ranging from 0.1 to 100 ng. 
Amplification plot and standard curve in the assay for detection of t(14;18); positive KARPAS 422 were used to generate 5 standards ranging from 0.1 to 1000 ng. 
Article
Healthy radio-exposed individuals who received low levels of Cesium-137 radiation during the accident that occurred in Goiânia in 1987, their families and controls were tested for the detection of t(14;18)-rearranged B cells in peripheral blood by using a highly sensitive, real-time quantitative PCR method. The chromosomal translocation t(14;18)(q32;q21) is characteristic of follicular lymphoma and is a frequent abnormality observed in other types of non-Hodgkin's lymphoma. This translocation leads to constitutive activation of the BCL2 oncogene by the enhancers of the immunoglobulin heavy-chain locus. In healthy individuals, the same translocation may also be found in a small fraction of peripheral blood lymphocytes, and positive cells might serve as an indicator for environmental exposure to carcinogens and possibly correlate with the cumulative risk of developing t(14;18)- positive non-Hodgkin's lymphoma. Twenty healthy radio-exposed individuals, 10 relatives and 10 non-exposed healthy individuals were tested for the detection of this translocation. Only 1 non-exposed individual was positive for the chromosomal translocation, and healthy radio-exposed individuals presented lower levels of cells bearing the BCL2/J(H) rearrangement when compared to the levels of the patients with follicular lymphoma before treatment. However, evaluation of more cells would be required to confirm the total absence of circulating cells bearing BCL2/J(H) rearrangement.
 
a. G-banded normal and derivative chromosome 4 from the fetus. b. Metaphase spread painted for chromosomes 4 and 13 demonstrating the additional material's origin as being from chromosome 13.  
Array comparative genomic hybridization spectral view of chromosome 13 (A) and 4 (B) of the fetus (Constitutional Chip 4.0).  
Article
Partial trisomy 13q is an uncommon chromosomal abnormality with variable phenotypic expression. We report prenatal diagnosis of partial trisomy 13q in a fetus with partial agenesis of the cerebellar vermis, partial agenesis of the corpus callosum, hydrops and polyhydramnios. G-banding karyotyping, spectral karyotyping and array comparative genomic hybridization (aCGH) analysis of fetal blood were performed. Cytogenetic analysis of fetal blood displayed 46,XX,add(4)(q28). The parental karyotypes were normal. A girl was delivered at 34 weeks gestation; she died within 2 h. Autopsy confirmed all the prenatal findings and also showed agenesis of the diaphragm. Spectral karyotyping identified the additional material's origin as chromosome 13. aCGH was carried out and showed amplification of distal regions of the long arm of chromosome 13 from region 13q14 to qter. This is the first report of a fetus with molecular characterization of a partial trisomy 13q (q14-->qter), present as a de novo unbalanced translocation at chromosome 4q. This case demonstrates the usefulness of molecular characterization of malformed fetuses for prenatal diagnosis and counseling.
 
Clinical manifestations. A. Large forehead, small nose with anteverted nares, prominent short philtrum, large mouth with downturned angles, widely spaced nipples, and short sternum. B. Prominent low-set posteriorly rotated ears, retrognathia. 
Father’s 3 and 13 chromosomes at band level 550. 
Article
We examined a girl presenting neuropsychomotor developmental delay and multiple malformations including antenatal and postnatal growth retardation, congenital heart defect, and facial dysmorphisms. Cytogenetic analysis was performed on peripheral blood lymphocytes with the GTG-banding technique, which revealed an unbalanced translocation: 46,XX,der(13)(13pter→13q34::3p24→3pter)pat. Karyotype analysis of the father demonstrated a balanced translocation, 46,XY,t(3;13)(p24;q34), indicating the inheritance of the derivative chromosome 13. The mother karyotype was normal. We suggest that most of the structural malformations seen in this patient are due to the 3p trisomy, while the neuropsychomotor alterations are a consequence of both chromosome aberrations.
 
Location and extent of chromosome 16p11.2 deletions. A UCSC Genome Browser (March 2006 (hg18) assembly) view of the chromosomal region 16p11.2 (chr16: 28,500,000-30,500,000) is shown, together with Refseq genes and segmental duplications. The bottom panel shows the location and extent of the 200-kb (the patient reported here) and 600-kb deletions in 16p11.2. 
Location and extent of chromosome 13q31.3 deletions. A UCSC Genome Browser (March 2006 (hg18) assembly) view of the chromosomal region 13q31.3 (chr13: 90,500,000-94,000,000) is shown, together with FISH clones, Refseq genes and segmental duplications. The bottom panel shows the location and extent of the 13q31.3 deletion in the patient described here (indicated by an asterisk), and of the case reported by Bachmann-Gagescu et al. (2010). 
Article
Chromosome microarray analysis of patients with developmental delay has provided evidence of small deletions or duplications associated with this clinical phenotype. In this context, a 7.1- to 8.7-Mb interstitial deletion of chromosome 16 is well documented, but within this interval a rare 200-kb deletion has recently been defined that appears to be associated with obesity, or developmental delay together with overgrowth. We report a patient carrying this rare deletion, who falls into the latter clinical category, but who also carries a second very rare deletion in 13q31.3. It remains unclear if this maternally inherited deletion acts as a second copy number variation leading to pathogenic variation, or is non-causal and the true modifiers are yet to be determined.
 
Article
Extended-spectrum β-lactamases (ESBLs) and AmpC β-lactamases produced by a clinical isolate of Klebsiella pneumoniae from chickens were detected with confirmatory phenotypic tests of the Clinical and Laboratory Standards Institute. The minimum inhibitory concentrations of 18 antibacterial drugs against K. pneumoniae were determined by the 2-fold microdilution method. The genotype and subtype of the ESBL-producing and AmpC β-lactamase-producing K. pneumoniae isolate were identified by PCR amplification of the enzyme-encoding genes followed by DNA sequencing analysis. K. pneumoniae K(1) isolate was an ESBL-producing and AmpC β-lactamase-producing bacteria with high resistance to β-lactam antibiotics, such as penicillins, third-generation cephalosporins, fluoroquinolones, and aminoglycosides. The sequence analysis showed that K. pneumoniae K(1) harbored TEM-type, SHV-type, CTX-M-type, and ACT-type AmpC β-lactamase nucleotide sequences. The TEM-type sequence was designated as TEM-1; the SHV-type sequence was designated as SHV-11; the CTX-M-type sequence was designated as CTX-M-14. Compared with the ACT-like sequence (EF078894), the ACT-type sequence was characterized by 8 nucleotide mutations (A(75)G, C(84)G, T(90)C, A(105)G, G(213)A, G(246)A, C(309)T, and T(315)C). Only one mutation at position 75 led to an amino acid substitution (Asn28Lys). The bla(ACT) type was an ACT-like derivative.
 
Article
We looked at how zinc transporter 3 ZnT-3) mRNA expression in the rat retina is affected by low dietary zinc. Groups of 12 four-week-old male Sprague Dawley rats were fed on a low-zinc diet for 2, 4 or 6 weeks. Half of each group was then fed with a normal-zinc content diet and the other half was given a low-zinc content diet. The expression of ZnT-3, carbonic anhydrase 2 (CA2) and 14 (CA14) were detected by RT-PCR. After the rats were fed a low-zinc content diet for 2 weeks, their retina CA2 and CA14 mRNA levels were decreased, and the ZnT-3 mRNA was increased compared with the control rats. After they were fed a low-zinc diet for 4 weeks, ZnT-3, CA2 and CA14 mRNA levels decreased significantly. Then, after being changed back to a normal diet for 2 weeks, the rats had ZnT-3, CA2 and CA14 mRNA levels recovery in the retina.
 
Article
Several lines of evidence suggest that the dopaminergic system is involved in the pathophysiology of major depressive disorder (MDD). Since the dopamine transporter (DAT1, also known as SLC6A3), mediates the active reuptake of dopamine from the synapses and thereby plays a vital role in the regulation of dopaminergic neurotransmission, we looked for a possible association between the C/T single nucleotide polymorphism in intron 14 of the DAT1 gene (also referred to as rs40184) and MDD in a northeastern Thai population. One hundred and seventy-eight patients with MDD and 205 unrelated healthy controls were included in our study. Genotyping was performed using our newly established polymerase chain reaction-restriction fragment length polymorphism technique. We found no significant differences in genotype distributions, allele frequencies and allele carrier frequencies when comparing the two groups. Although not significant, we observed more carriers of the C allele (CC+CT genotypes) in healthy controls than in patients with MDD (chi(2) = 3.20, degrees of freedom = 1, P = 0.073, odds ratio = 0.53 [95% confidence interval = 0.28-1.01]). We also detected significant differences in the allele frequencies of rs40184 between healthy subjects of Asian ancestry and those of both Caucasian and African ancestry. We concluded that there is a tendency towards an association between the homozygous TT genotype of the rs40184 single nucleotide polymorphism and an increased risk for MDD in this northeastern Thai population. Possibly, with more samples, this tendency will be confirmed.
 
Article
Spontaneous mutations are a common phenomenon, occurring in both germ-line and somatic genomes. They may have deleterious consequences including the development of genetic disorders or, when occurring in somatic tissues, may participate in the process of carcinogenesis. Similar to many mutational hotspots, the G1138A mutation in the fibroblast growth factor receptor 3 (FGFR3) gene occurs at a CpG site. In germ-line tissues, the G1138A mutation results in achondroplasia and has one of the highest spontaneous mutation rates in the human genome. Although not at the G1138A site, there are increased rates of other somatic mutations in the FGFR3 gene that have been reported in multiple myeloma cases associated with a translocation, t (4; 14). The chromosome-4 break points in this translocation are clustered in a 70-kb region centromeric to the FGFR3 gene. We hypothesized that this translocation may impact the mutation rate at the G1138A site. We employed a semi-quantitative polymerase chain reaction-based assay to measure the frequency of this mutation in multiple myeloma cell lines carrying t (4; 14) translocation. Analysis of these cell lines varied from no change to a 10-fold increase in the mutation frequency compared with normal controls. In general, there was an increase in the G1138A mutational frequency suggesting that chromosomal rearrangement can affect the stability of the CpG hotspots.
 
Evolution of the means obtained in the cycles C 0 , C 1 , C 2 , C 3 , C 4 , C 5 , C 6 , and predicted in C 7 for the traits grain yield (kg/ha). 
Article
The popcorn breeding program of Universidade Estadual do Norte Fluminense Darcy Ribeiro aims to provide farmers a cultivar with desirable agronomic traits, particularly with respect to grain yield (GY) and popping expansion (PE). We evaluated full-sib families from the seventh cycle of recurrent selection and estimated the genetic progress with respect to GY and PE. Eight traits were evaluated in 200 full-sib families that were randomized into blocks with two replicates per set in two contrasting environments, Campos dos Goytacazes and Itaocara, located in north and northwest Rio de Janeiro State, respectively. There were significant differences between sets in families with respect to all traits evaluated, which indicates genetic variability that may be explored in future cycles. Using random economic weights in the selection of superior progenies, the Mulamba and Mock index showed gains for PE and GY of 5.11 and 7.78%, respectively. Significant PE and GY increases were found when comparing the evolution of mean values of these two parameters that were assessed at cycles C0-C6 and predicted for C7. Thus, an advanced-cycle popcorn cultivar with genotypic superiority for the main traits of economic interest can be made available to farmers in Rio de Janeiro State.
 
Article
Endometriosis is a chronic gynecological disease defined as the presence of the endometrium outside the uterine cavity. Endometriosis is a multifactorial and polygenic disease in which angiogenesis may be implicated. Angiogenesis is under the control of numerous inducers, including vascular endothelial growth factor (VEGF). Many studies have reported that VEGF plays a role in the progression of the disease, but individually published studies showed inconclusive results. We investigated the association between VEGF polymorphisms and the susceptibility to endometriosis. The MEDLINE, EMBASE, Web of Science, and CBM databases were searched for all articles published up to June 25, 2012, which addressed VEGF polymorphisms and endometriosis risk. We investigated the potential association between VEGF polymorphisms and the risk of endometriosis. Fourteen studies were included with a total of 3313 endometriosis cases and 3393 healthy controls. Meta-analysis results showed that the rs699947 (A>C) and rs1570360 (G>A) polymorphisms in the VEGF gene were associated with a decreased risk of endometriosis, while rs3025039 (C>T) might increase the risk of endometriosis. However, the rs833061 (T>C) and rs2010963 (G>C) polymorphisms of the VEGF gene did not appear to have an influence on endometriosis susceptibility. Results from the meta-analysis suggest that the rs3025039 (C>T) polymorphism of the VEGF gene increases the risk of endometriosis, but the rs699947 (A>C) and rs1570360 (G>A) polymorphisms might be protective factors for endometriosis.
 
Article
ORFs 10 and 14 from Bombyx mori multiple nucleopolyhedrovirus (BmMNPV) were amplified, cloned and sequenced. Nucleotide analysis of these genes and those of other baculoviruses showed that these genes are highly conserved. The p10 protein from BmMNPV ORF10 has 70 amino acid residues similar to that of the four other known BmNPV strains. The BmMNPV ORF14 alignment showed a higher identity with the nucleopolyhedrovirus ORF14 from the baculovirus BmNPV and from Autographa californica multiple nucleopolyhedrovirus. The BmMNPV ORF14 protein has a putative transmembrane domain in the C-terminal region, which is similar to that of other baculoviruses. A phylogenetic analysis showed that BmMNPV ORF14 protein has higher similarity with BmNPV ORF14 and ORF23 of A. californica multicapsid nucleopolyhedrovirus (Ac23). We conclude that proteins produced by ORFs 10 and 14 from BmNPV and BmMNPV are highly conserved in NPVs and MNPVs. The high degree of conservation among members of these genera indicates the importance of these proteins, which could mean an important function that is active throughout the infection cycle.
 
Article
Expression of serotonin 2A receptor (5-HTR2A) is known to increase in psoriasis, a chronic inflammatory skin disease. We investigated a possible association between the -1438A/G single nucleotide polymorphism (rs6311) in the promoter region of 5-HTR2A gene and psoriasis in a Thai population. One hundred and twelve psoriatic patients and 151 unrelated healthy controls were included in our study. Genotyping was performed using the polymerase chain reaction and restriction fragment length polymorphism techniques. We found no overall differences in genotype distributions and allele frequencies when comparing between the two groups. When we analyzed a subset of psoriatic patients classified by onset and severity, only the -1438A allele was significantly increased in patients with late-onset psoriasis when compared with the healthy control group (chi(2) = 4.77, d.f. = 1, P = 0.029, odds ratio = 2.298 [95% confidence interval = 1.126-4.691]). This single nucleotide polymorphism may be involved in late-onset psoriasis in this Thai population.
 
Article
Several lines of evidence suggest a molecular role of -1438A/G single nucleotide polymorphism in the 5-HTR2A gene promoter (rs6311) in regulating the expression of this gene, making rs6311 polymorphism a promising candidate for an association study. We looked for a possible association between rs6311 polymorphism and major depressive disorder (MDD) in a northeastern Thai population. We included 180 patients with MDD and 183 unrelated healthy controls in our study. Genotyping was performed using PCR-RFLP. We found no significant differences between the two groups with regard to both genotype distributions (chi(2) = 1.32, d.f. = 2, P = 0.516) and allele frequencies (chi(2) = 0.01, d.f. = 1, P = 0.913, odds ratio = 0.96, 95% confidence interval = 0.67-1.39). Therefore, this single nucleotide polymorphism appears not to be involved in the etiology of MDD.
 
A. Circulatory microRNA-145 expression profile of ischemic stroke patients, N = 32. B. Paired expression profile of patients, N = 11. Peripheral blood was resampled and expression profile of circulatory microRNA-145 was generated and compared. Expression values are normalized to the mean of the expression values from healthy controls. All values are reported as mean fold changes ± standard error of the mean, and P < 0.05 is considered to be significant.
Effect of microRNA-145 congregate on serum response factor (SRF)-dependent transcription by regulation of co-activators and co-repressors directing cell fate. MicroRNA-145 potentiates myocardin (Myocd) and negatively regulates Kruppel-like factor (KLF4/5), which interacts with SRF and also inhibits Myocd. KLF is a transcription factor implicated in pluripotency. ETS-like transcription factor 1 (Elk-1) represses Myocd's activity by competing for common docking site (displacing Myocd from SRF), activating gene transcription for cell dedifferentiation. Upregulation of microRNA-145 renders Myocd functional in directing cell differentiation by repressing KLF4/5 and potentiates Myocd's effect over Elk-1 (Long et al., 2008; Cheng et al., 2009; Cordes et al., 2009).
Article
Cerebral ischemia or ischemic stroke is mainly attributed to vascular and circulation disorders. Among protein biomarkers, RNA profiles have also been identified as markers of ischemic stroke. MicroRNA-145 expression is ostensibly recognized as marker and modulator of vascular smooth muscle cell phenotype; however, expression levels in ischemic stroke had not been investigated. Employing real-time quantitative PCR, we examined the expression profile of circulatory microRNA-145 in healthy control subjects (N = 14) and ischemic stroke patients (N = 32). Circulatory microRNA-145 expression was significantly higher in ischemic stroke patients than in control subjects. This demonstrates that hemostatic mechanisms are affected by ischemic stroke. We conclude that circulating microRNA-145 has potential as a biomarker for ischemic stroke.
 
Top-cited authors
Yves Le Loir
  • French National Institute for Agriculture, Food, and Environment (INRAE)
Florence Baron
  • Agrocampus Ouest
Antônio Teixeira do Amaral Júnior
  • Universidade Estadual do Norte Fluminense
Leandro Simões Azeredo Gonçalves
  • Universidade Estadual de Londrina
José Bento Sterman Ferraz
  • University of São Paulo