Table of Contents | Genet. Mol. Res. 2016 (3)
The WRKY family is one of the most important transcription factor families in plants, involved in the regulation of a broad range of biological roles. The recent releases of whole-genome sequences of pepper (Capsicum annuum L.) allow us to perform a genome-wide identification and characterization of the WRKY family. In this study, 61 CaWRKY proteins were identified in the pepper genome. Based on protein structural and phylogenetic analyses, these proteins were classified into four main groups (I, II, III, and NG), and Group II was further divided into five subgroups (IIa to IIe). Chromosome mapping analysis indicated that CaWRKY genes are distributed across all 12 chromosomes, although the location of four CaWRKYs (CaWRKY58-CaWRKY61) could not be identified. Two pairs of CaWRKYs located on chromosome 01 appear to be tandem duplications. Furthermore, the phylogenetic tree showed a close evolutionary relationship of WRKYs in three species from Solanaceae. In conclusion, this comprehensive analysis of CaWRKYs will provide rich resources for further functional studies in pepper.
Activity of methylenetetrahydrofolate reductase (MTHFR), an enzyme involved in folate metabolism, is influenced by mutations in the corresponding gene, contributing to a decrease in 5,10-MTHF. Due to such polymorphisms, individuals differ in MTHFR enzyme activity and plasma folate levels. We investigated the relationship between two common MTHFR polymorphisms (C677T and A1298C) and breast cancer (BC) chemotherapy response. From February 2013 to January 2016, 148 advanced BC patients at the Center Hospital of Cangzhou were enrolled and treated with six different chemotherapy regimens. Subjects were genotyped using polymerase chain reaction-restriction fragment length polymorphism. Forty-one (27.7%), 70 (47.3%), and 37 (25.0%) patients carried the C/C, C/T, and T/T C677T genotypes, respectively; 101 (68.2%), 42 (28.4%), and 5 (3.4%) had the A/A, A/C, and C/C genotypes of A1298C, respectively. Total chemotherapy efficacy was 66.9% (99/148), with 7 (4.7%), 92 (62.2%), 36 (24.3%), and 13 (8.8%) cases showing complete response, partial response, no change, and progressive disease, respectively. Chemotherapy regimens did not differ in effectiveness (P > 0.05). Efficacy rates associated with C677T C/C, C/T, and T/T genotypes were 58.5, 58.6, and 91.9%, respectively, with T/T carriers exhibiting significantly better responses than the C/C (P 0.05). The MTHFR C677T genotype may be associated with BC chemotherapy response, and could be of great value in guiding individualized treatment for this disease.
miRNA-203 is involved in the development and progression of various types of cancer. However, its role in cervical cancer remains unclear. The aim of this study was to investigate the effect of miRNA-203 on the proliferation and migration of HeLa cervical cancer cells, as well as survivin expression in these cells. A miRNA-203 primer probe was designed according to a sequence obtained from NCBI. The expression of miRNA-203 in cervical epithelial cells and cervical cancer cells was detected by quantitative reverse transcriptase-polymerase chain reaction. The miRNA-203 expression pattern was compared between these two cell lines. The cervical cancer cells were transfected with miRNA-203 mimic or inhibitor to determine their effects on proliferation and migration. The expression of the miRNA-203 target protein (survivin) was analyzed by western blot. Cervical cancer cells showed reduced miRNA-203 expression compared to cervical epithelial cells. Transfection of miRNA-203 mimic upregulated the expression of miRNA-203, suppressed cell proliferation and migration, and downregulated survivin expression (P 0.05). In conclusion, upregulation of miRNA-203 in cervical cancer cells inhibits the proliferative and migratory capacities of these cells by downregulating the expression of survivin.
Human colorectal cancer (CRC) is a major worldwide health concern, and its development has been shown to be associated with alcohol intake. We carried out a study to investigate the effect of the ADH1B Arg47His and ALDH2 Glu487Lys genetic polymorphisms and their interaction with alcohol consumption on development of CRC. Between March 2013 and May 2015, a total of 274 CRC patients and 358 healthy controls were recruited. Genotyping of sequence variations was performed using the polymerase chain reaction-restriction fragment length polymorphism method. Under a co-dominant model, individuals with the ADH1B Arg47His AA genotype showed increased CRC risk compared to those carrying the GG genotype, with an adjusted odds ratio (and 95% confidence interval) of 3.37 (2.00-5.70). Moreover, under dominant and recessive models, ADH1B Arg47His variant genotypes were associated with greater susceptibility to CRC when compared with the wild-type sequence. Both polymorphisms examined were positively associated with alcohol consumption in a Spearman correlation analysis of CRC risk. In conclusion, our study suggests that the ADH1B Arg47His polymorphism, but not the ALDH2 Glu487Lys variation, may influence development of CRC in the Chinese population.
Simple sequence repeats (SSRs), one of the most powerful molecular markers, can be used for DNA fingerprinting, variety identification, genetic mapping, and marker-assisted selection. Using the pear’s (Pyrus pyrifolia Nakai) 75,764 unigenes (55,676,271 bp) obtained by deep transcriptome sequencing, a total of 10,622 novel SSRs were identified in 9154 unigenes, accounting for 14.02% of all unigenes. The average length and distribution of these SSRs was about 16 bp and 5.24 kb, respectively. Dinucleotide repeat motifs were the main type, with a frequency of 55.87%, followed by trinucleotides (24.45%). There were 159 kinds of repeat motifs existing in the pear transcriptome. AG/CT was the most frequent motif, accounting for 49.64%. All 9154 SSR-containing unigenes were functionally annotated using Nr (NCBI non-redundant protein database), Nt (NCBI non-redundant nucleotide database), and the Swiss-Prot database, and were classified further by Gene Ontology and Clusters of Orthologous Groups. In addition, a total of 4300 primer pairs were designed from all SSR loci obtained. Of these, 40 primers were randomly selected for PCR amplification and polyacrylamide gel (PAGE) analysis. Among the 40 primer pairs, 31 were successfully separated via PAGE. These findings also confirm that mining SSRs using next-generating sequencing technologies is a fast, effective, and reliable approach.
This study was undertaken primarily to develop new simple sequence repeat (SSR) markers for Capsicum. As part of this project aimed at broadening the use of molecular tools in Capsicum breeding, two genomic libraries enriched for AG/TC repeat sequences were constructed for Capsicum annuum. A total of 475 DNA clones were sequenced from both libraries and 144 SSR markers were tested on cultivated and wild species of Capsicum. Forty-five SSR markers were randomly selected to genotype a panel of 48 accessions of the Capsicum germplasm bank. The number of alleles per locus ranged from 2 to 11, with an average of 6 alleles. The polymorphism information content was on average 0.60, ranging from 0.20 to 0.83. The cross-species transferability to seven cultivated and wild Capsicum species was tested with a set of 91 SSR markers. We found that a high proportion of the loci produced amplicons in all species tested. C. frutescens had the highest number of transferable markers, whereas the wild species had the lowest. Our results indicate that the new markers can be readily used in genetic analyses of Capsicum.
Pseudomonas aeruginosa is one of the most important causes of nosocomial infection and it has increasing resistance to many antimicrobial agents. β-lactamase production is the most frequent mechanism for β-lactam resistance in P. aeruginosa. We evaluated the prevalence of β-lactamase genes in P. aeruginosa for classes A, C, and D by polymerase chain reaction, and investigated clonal diversity by pulsed-field gel electrophoresis (PFGE). We used the disk diffusion method to test 118 non-duplicate clinical isolates of P. aeruginosa for antimicrobial susceptibility. We identified 51 isolates (43.22%) as multidrug-resistant P. aeruginosa, approximately 44.91% of which were resistant to ceftazidime. β-lactamase genes were found in 80 isolates of P. aeruginosa (67.80%). The genes that encode VEB-1, AmpC, and OXA-10 were detected in 9 (7.62%), 75 (63.56%), and 18 (15.25%) of these isolates, respectively. The genes that encode PER-1, CTX-M, TEM-1 and derivatives, and SHV-1 were not found in any of the P. aeruginosa isolates. We identified 29 different pulsotypes by PFGE. Two predominant pulsotypes were found. In pulsotype 1, OXA- 10, which was co-produced with the AmpC gene, was predominant. Moreover, VEB-1-producing strains were found to be scattered in many pulsotypes, and AmpC-producing strains showed high pulsotype diversity. The prevalence of β-lactamase genes in P. aeruginosa was represented by the genetic heterogeneity of OXA-10, AmpC, and VEB-1. The predominant clone of P. aeruginosa clinical isolates was OXA-10. This raises concern about oxacillinases among P. aeruginosa clinical isolates.
Hand-foot-mouth disease (HFMD) is a common pediatric disease responsible for the development of rashes or herpes on the hand, foot, and mouth. Severe complications of HFMD include myocarditis, pulmonary edema, aseptic meningoencephalitis, and even death. Therefore, early diagnosis of HFMD is of particular importance. In this study, we determined the clinical value of the combined detection of liver function and high-sensitivity C-reactive protein (hs-CRP) expression in children with HFMD. Three hundred children with HFMD were recruited to this study between July 2013 and July 2015 and divided into the mild and severe HFMD groups (N = 150 per group). The liver function [aspartate aminotransferase (AST), alanine transaminase (ALT), and alkaline phosphatase (ALP) levels] and hs-CRP expression were evaluated using standardized tests, and the clinical value of combined detection of these indices (in parallel and serially) was determined. Patients in the severe HFMD group showed significantly higher levels of ALT, AST, ALP, and hs-CRP compared to those in the mild HFMD group (P
Previous studies have shown a close correlation between the generation of B cell autoantibodies and imbalances in T lymphocyte subpopulations and the occurrence of disease. In this study, we have analyzed the effects of abnormal expression of CD4+CD25+-regulatory T cells, T lymphocyte subpopulations, immunoglobulins, complement factors, inflammatory factors, and adhesion molecules in the peripheral blood on the occurrence and development of autoimmune disease. Eighty patients with autoimmune disease were randomly (equally) divided into active-stage and stable-stage disease groups (according to pre-defined criteria). Fifty healthy people were recruited to the control group. The above-mentioned indices were detected by flow cytometry, immunity transmission turbidity, and enzyme-linked immunosorbent assay. We observed an obvious decrease in the CD4+CD25+- regulatory T cell, CD4+ cell, CD4+/CD8+ cell, NK cell, C3, and C4 expression in all three groups; however, this decrease was statistically significant in the active-stage group (P
Copper-transporting P-type adenosine triphosphatase (ATP7B) has been identified as the pathogenic gene in hepatolenticular degeneration, or Wilson’s disease (WD). The aim of this study was to explore the correlation between genetic mutations and the clinical profile of WD, and to discuss the value of mutation examination in its diagnosis for providing a scientific basis for the development of a method to examine genetic mutations. Sixty-eight Chinese Han patients with WD and 20 controls were included in this study. The ATP7B gene in DNA extracted from patient blood samples was amplified by PCR and sequenced. These sequences were compared against corresponding gene sequences obtained from healthy controls to statistically analyze the genetic mutations. Five of the nineteen mutations in ATP7B were newly detected mutations; moreover, 8 of these mutations were polymorphic (2 were newly identified). The Arg778Leu and Pro992Leu mutations in exons 8 and 13 were detected at the highest mutation frequencies of 25.74 and 16.91%, respectively. The frequencies of all other mutations were below 5%. However, the clinical manifestations of WD did not differ significantly in patients with the Arg778Leu and Pro992Leu mutations. Therefore, these mutations were considered as hotspot mutations in Chinese WD patients. However, we observed no significant correlation between these genetic types and the clinical symptoms of WD. The correlation between the mutation genotype and disease phenotype remains to be elucidated. In conclusion, the highly sensitive and specific direct DNA sequencing method can be used to screen for the causative genes of WD.
The aim of this study was to identify inbred progenies of S0:1 maize (Zea mays L.) plants that were efficient at a low level of technology and responsive at a high level of technology through the use of topcrosses. Two contrasting environments were created using two levels of base fertilization and topdressing, so that the levels of nitrogen, phosphorus, and potassium were applied four times higher in one environment than in the other. We used S0:1 progenies derived from commercial hybrids in topcrosses with two testers (an elite line from the flint heterotic group and an elite line from the dent heterotic group). The progenies and three controls were evaluated in an augmented block design in Nossa Senhora das Dores, SE, Brazil in the 2010 crop season. The average grain yield in the high-technological level was 21.44% greater than that in the low-technological level. There were no changes in progeny behavior in the two technological levels for grain yield. The testers did not differ in the average grain yield of the progenies at the two technological levels. Therefore, it is possible to select progenies derived from commercial hybrids that have an efficient response to fertilization.
The domestication of the Equus genus 5000-6000 years ago has influenced the history of human civilization. As soon as horse and donkey species had been domesticated, they were crossbred, producing humanity’s first documented attempt at animal genome manipulation. Since then, the mule (male donkey x female horse) and the reciprocal cross (the hinny, male horse x female donkey) have been the most common equine hybrids in the world. Due to their hybrid vigor, mules and hinnies have been intensively used for carrying loads and people and for tilling the land. Despite their importance, visual distinction of mules and hinnies is difficult due to high phenotypic resemblance. However, the distinction between these two hybrids is of pivotal importance for equid breeders and ranchers. In this study, an easy, low-cost, effective, and fast multiplex-polymerase chain reaction method was developed to distinguish the maternal origin of mules and hinnies, targeting the hyper-variable mitochondrial DNA D-loop region. This methodology can help breeders, ranchers, animal science professionals, and researchers manage their equine herds with more confidence and precision.
v-myb avianmyeloblastosis viral oncogene homolog (MYB) transcription factors are key regulators of stress responsive gene expression in plants. In this study, the MYB gene, ChiMYB (GenBank accession No. KT948997), was isolated from Chrysanthemum indicum, and was functionally characterized with an emphasis on salinity stress tolerance. The full ChiMYB cDNA sequence (948 bp) encoded a typical R2R3 MYB transcription factor that contained 315 amino acid residues and two MYB domains. The temporal expression pattern of ChiMYB was noted in C. indicum, and the highest level was detected in the roots, followed by leaves and stems. ChiMYB expression was induced by NaCl treatments, and transient expression of the fusion of ChiMYB and green fluorescent protein (GFP) indicated that the protein was targeted to the nuclei of onion epidermal cells. Arabidopsis plants overexpressing ChiMYB displayed improved tolerance to drought and salt stress. When under salt stress conditions, transgenic Arabidopsis plants had higher survival rates than non-transgenic wild-type plants. Chlorophyll content, intercellular CO2 concentration, photosynthetic rate, and stomatal conductance were higher in the transgenic Arabidopsis plants than in non-transgenic control plants. Further investigation revealed that ChiMYB was able to regulate the expression of RD29A, RAB18, COR15, ABI1, and ABA genes, which are involved in salt stress signaling pathways. Our findings demonstrated that ChiMYB is essential for plant responses to salt stress, and it may have great potential for the improvement of salt tolerance in crops.
Fusarium oxysporum strain BM-201 was treated with ultraviolet (UV) radiation to obtain a high pectinase-producing strain. Mutant UV-10-41 was obtained and then treated by diethyl sulfate. Next, the mutant UV-diethyl sulfate-43 derived from UV-10-41 was selected as high pectinase-producing strain. Mutant UV-diethyl sulfate-43 was incubated on slant for 10 generations, demonstrating that the pectinase-producing genes were stable. Pectinase activity reached 391.2 U/mL, which is 73.6% higher than that of the original strain.
Nontuberculous mycobacteria are ubiquitous in outside environment and animals. As for nontuberculous mycobacteria infection, there is only limited information in humans regarding infection and the subsequent immune response, especially for Mycobacterium neoaurum. Here, haematoxylin-eosin and Ziehl-Neelsen staining were used to observe pathological changes and detect acid-fast bacilli in organ samples in mouse model. Flow cytometry and quantitative real-time polymerase chain reaction were performed to analyze the contribution of Th1, Th17 and Tregs to the host immune response. M. neoaurum caused chronic infection in mice, resulting in infiltrates with large aggregates of inflammatory cells, especially macrophages, in lung tissues. Our results indicated that 72% of CD4+ T cells appeared in the early days of infection, which was followed by a decrease to 47% by day 32, and then a rise to 76% by day 56. Moreover, we found higher frequency of IFN-g-producing CD4+ T cells and elevated mRNA expression of the transcription factor T-bet in the lungs; however, we observed lower mRNA expression of the transcription factor RORgt and lower frequency of IL-17-producing CD4+ T cells. A transient relative decrease in the number of Treg cells was observed in the lungs; however, the number of Tregs did not change significantly between the first and last day following infection. Thus, M. neoaurum causes chronic infection in C57BL/6 mice, with Th1, Th17, and Tregs playing a prominent role in the host response. The present study may lay the basis for further studies on the mechanisms underlying infection with nontuberculous mycobacteria.