PURPOSE: The purpose of this study is to evaluate the correlations between the multidrug resistance-associated protein (MRP) and multidrug resistance (MDR1) gene in osteosarcoma, and their prognostic significances by RT-PCR method. MATERIALS AND METHODS: We isolated RNA from 34 fresh deep-frozen primary osteosarcoma tissue specimens and evaluated the expression level of MRP and MDR1 m-RNA using RT-PCR method. GAPDH was used as the housekeeping gene for the experiment. RESULTS: The average MRP/GAPDH m-RNA ratio was 0.550 and the average MDR1/GAPDH m-RNA ratio was 0.419. There were moderate degree of correlations between MRP/GAPDH m-RNA and MDR1/GAPDH m-RNA ratio (p<0.05). There was significant correlations between the chemotherapy response and the MDR1/GAPDH m-RNA ratio (p<0.05), but not with the MRP/GAPDH ratio. Multivariate analysis for the correlation between the MRP and MDR1 gene expression and the chemotherapy response revealed that only the MDR1/GAPDH m-RNA ratio was significantly related to it (p<0.05). CONCLUSION: There was a moderate degree of correlation between the expressions of MRP and MDR1 genes. However, the chemotherapy response showed significant correlations with the expression of MDR1 gene, but not with MRP gene.
Drug Resistance, Multiple* ; Drug Therapy ; Gene Expression* ; Genes, Essential ; Genes, MDR ; Multidrug Resistance-Associated Proteins* ; Multivariate Analysis ; Osteosarcoma* ; RNA

Congenital aniridia is a rare ocular malformation that presents with severe hypoplasia of the iris and various ocular manifestations. Most cases of congenital aniridia are known to be related to mutations in the paired box gene-6 (PAX6), which is an essential gene in eye development. Herein, we report a familial case of autosomal dominant congenital aniridia with four affected members in 3 consecutive generations and describe the detailed ophthalmologic findings for one of these members. As expected, mutational analysis revealed a nonsense mutation (p.Ser122*) in the PAX6 gene. Thus, our findings reiterate the importance of PAX6 mutations in congenital aniridia.
Aniridia* ; Codon, Nonsense ; Family Characteristics ; Genes, Essential ; Humans ; Iris ; WAGR Syndrome ; Wilms Tumor

Microbial genome reduction and modification are important strategies for constructing cellular chassis used for synthetic biology. This article summarized the essential genes and the methods to identify them in microorganisms, compared various strategies for microbial genome reduction, and analyzed the characteristics of some microorganisms with the minimized genome. This review shows the important role of genome reduction in constructing cellular chassis.
Genes, Essential ; genetics ; Genetic Engineering ; Genome, Microbial ; genetics ; Synthetic Biology ; methods

The present study was conducted to determine the full rpoB and eight house-keeping gene sequences of 78 and 35, respectively, avian pathogenic E. coli (APEC) strains. Phylogenetic comparison with 66 E. coli and Shigella strains from GenBank and EMBL was also conducted. Based on the full rpoB sequence, 50 different rpoB sequence types (RSTs) were identified. RST 1 was assigned to a major RST that included 34.7% (50/144) of the analyzed strains. RST 2 to RST 50 were then assigned to other strains with higher nucleotide sequence similarity to RST 1 in order. RST 1, 11, and 23 were mixed with APEC along with human commensal and pathogenic strains while RST 2, 6, 9, 13-15, 22, 24, 25, 33, 34, 36, and 41 were unique to APEC strains. Only five APEC strains grouped into RST 32 and 47, which contained human pathogenic E. coli (HPEC). Thus, most of the APEC strains had genetic backgrounds different from HPEC strains. However, the minor APEC strains similar to HPEC should be considered potential zoonotic risks. The resolution power of multi-locus sequence typing (MLST) was better than RST testing. Nevertheless, phylogenetic analysis of rpoB was simpler and more economic than MLST.
Base Sequence ; Databases, Nucleic Acid ; Escherichia coli* ; Genes, Essential ; Humans ; Shigella

Our research sought to characterize the phylogeny of Pseudomonas aeruginosa isolated from pet Chinese stripe-necked turtles (Ocadia sinensis) to better understand its evolutionary relation to other isolates and increase understanding of a potential zoonotic pathogen transmitted through direct contact with pet turtles. Thirty-one Pseudomonas aeruginosa isolates were obtained from both immature and adult turtles sold in pet shops in Korea. To characterize the phylogenic position of Chinese stripe-necked turtle-borne P. aeruginosa relative to other strains, multilocus sequence typing (MLST) analysis was performed due to the accessibility and breadth of MLST databases. Seven housekeeping genes (acsA, aroE, guaA, mutL, nuoD, ppsA, and trpE) were sequenced and the results were compared with data from the MLST database. The genes were further used for phylogenetic analysis of P. aeruginosa using concatenated gene fragments. Both rooted and unrooted phylogenetic trees were generated. Eleven distinct sequence types were present within the isolates among which seven were new. Expanding an unrooted phylogenetic tree to include P. aeruginosa MLST sequences isolated from various other geographic locations and sources revealed a divergent cluster containing the majority of isolates obtained from turtles. This suggests that P. aeruginosa strains particularly well-adapted for inhabiting turtles occupy a distinct phylogenetic position.
Adult ; Asian Continental Ancestry Group* ; Genes, Essential ; Geographic Locations ; Humans ; Korea ; Multilocus Sequence Typing* ; Phylogeny ; Pseudomonas aeruginosa* ; Pseudomonas* ; Trees ; Turtles*

Ribonucleic acid (RNA) has potential use in forensic science for the determination of postmortem interval. We report the first study on serial sampling of messenger RNA (mRNA) from surgical specimens to determine if there is a correlation between mRNA quantity and elapsed time. Skin tissues were collected from modified radical mastectomy specimens. After a defined period of time, bisected skin sections were cut and frozen in liquid nitrogen. Serial collection of the specimens was conducted, and frozen sections were obtained from all samples. Quantitative real-time reverse transcription-polymerase chain reaction was performed using the extracted RNA to measure the transcriptional activity of 2 selected housekeeping genes. The selected loci were mRNA sequences that exhibited time-dependent quantitative changes in a previous study. We collected 44 samples from 9 different patients, with 3-10 samples collected per patient. The amount of mRNA transcripts present in the serial samples showed a weak time-dependent correlation trend only in some cases. Further studies to evaluate different target mRNA sequences are necessary, as is exploration of additional methods to evaluate mRNA transcript degradation.
Forensic Sciences ; Frozen Sections ; Genes, Essential ; Humans ; Mastectomy, Modified Radical ; Nitrogen ; RNA ; RNA Stability ; RNA, Messenger ; Skin

The genes related to specific events or pathways in bacteria are frequently localized proximate to the genome of their neighbors, as with the structures known as operon, but eukaryotic genes seem to be independent of their neighbors, and are dispersed randomly throughout genomes. Although cases are rare, the findings from structures similar to prokaryotic operons in the nematode genome, and the clustering of housekeeping genes on human genome, lead us to assess the genomic association of genes as functional subunits. We evaluated the genomic association of neighboring genes on chromosomes 4 and 5 of Arabidopsis thaliana with and without respectively consideration of the scaffold/matrix-attached regions (S/MAR) loci. The observed number of functionally identical bigrams and trig rams were significantly higher than expected, and these results were verified statistically by calculating rho-values for weighted random distributions. The observed frequency of functionally identical big rams and trig rams were much higher in chromosome 4 than in chromosome 5, but the frequencies with, and without, consideration of the S/MAR in each chromosome were similar. In this study, a genomic association among functionally related neighboring genes in Arabidopsis thaliana was suggested.
Arabidopsis* ; Bacteria ; Chromosomes, Human, Pair 4 ; Chromosomes, Human, Pair 5 ; Genes, Essential ; Genome ; Genome, Human ; Humans ; Operon

BACKGROUND: Quantitative real-time polymerase chain reaction (qPCR) is the most reliable tool for gene expression studies. Selection of housekeeping genes (HKGs) that are having most stable expression is critical to carry out accurate gene expression profiling. There is no 'universal' HKG having stable expression in all kinds of tissues under all experimental conditions. METHODS: The present study aims to identify most appropriate HKGs for gene expression analysis in glioblastoma (GBM) samples. Based on literature survey, six most commonly used HKGs that are invariant in GBM were chosen. We performed qPCR using RNA from formalin fixed paraffin embedded GBM samples and normal brain samples to investigate the expression pattern of HPRT, GAPDH, TBP, B2M, B2M, RPL13A, and RN18S1 with different abundance. A simple Deltacycle threshold approach was employed to calculate the fold change. RESULTS: Our study shows that the expression of RPL13A and TBP were found to be most stable across all the samples and are thus suitable for gene expression analysis in human GBM. Except for TBP, none of the other conventionally used HKGs in GBM studies e.g., HPRT and GAPDH were found to be suitable as they showed variation in RNA expression. CONCLUSION: Validation of HKGs is therefore immensely specific for a particular experimental setup and is crucial in assessing any new setup.
Brain ; Formaldehyde ; Gene Expression Profiling ; Gene Expression* ; Genes, Essential* ; Glioblastoma* ; Humans ; Hypoxanthine Phosphoribosyltransferase ; Paraffin ; Real-Time Polymerase Chain Reaction* ; RNA

PURPOSE: Gene amplification/overexpression of c-erbB2/neu is controversy in BPH by conventional detecting methods. To evaluate the amplification and overexpression of c-erbB2/neu gene in BPH we have used and validated a one-step real time PCR and quantitative reverse transcription PCR assay based on fluorescent TaqMan methodology. MATERIALS AND METHODS: Using one-step real time PCR assay, we have assesed the amplification and overexpression of c-erbB2/neu gene in 30 prostate samples from patients with BPH as well as from 10 normal blood sample. Real time PCR and RT-PCR were performed on an iCycler (Bio-Rad Co., USA) and we used TaqMan probes to detect c-erbB2/neu transcripts amplified. All experiments were performed in duplicate using 96 well-PCR plate. The GAPDH housekeeping gene was used for normalization of c-erbB2/neu amplification and overexpression. RESULTS: In a series of 30 BPH samples c-erbB2/neu normalized amplification was found to range from 3.16 10(-3) to 7.16 10(-2) and overexpression to range from 7.72 10(-3) to 1.57 10. Sixteen cases of BPH (53.3%) showed c-erbB2/neu overexpression and only two cases (6.7%) showed amplification of c-erbB2/neu. Except 2 cases, no correlation was found between the results of amplification and overexpression of c-erbB2/neu (p=0.183). CONCLUSIONS: Our results using of one-step real time quantitative PCR assay suggest that a role of c-erbB2/neu overexpression in the development of BPH and the use of this new semi-automated technique will make molecular analysis of gene simpler and more reliable.
Equidae ; Gene Amplification* ; Genes, Essential ; Humans ; Polymerase Chain Reaction* ; Prostate ; Real-Time Polymerase Chain Reaction ; Reverse Transcription

BACKGROUND: Housekeeping genes, which show constant protein expression patterns between different tissue types, are very important in molecular biological studies as an internal control for protein research. METHODS: The protein expression profiles of seven housekeeping genes (HPRT1, PPIA, GYS1, TBP, YWHAZ, GAPDH and ACTB) in various rat tissues (cerebrum, cerebellum, cardiac ventricle and atrium, psoas muscle, femoral muscle, liver, spleen, kidney, and aorta) were analyzed by Western blot and compared by coefficient of variation (CV). RESULTS: HPRT1 was stably expressed (CV< or =10%) in six tissues (cerebrum, cerebellum, ventricle, femoral muscle, spleen, and kidney), PPIA was stably expressed in five tissues (cerebrum, cerebellum, ventricle, spleen and kidney), YWHAZ was stably expressed in three tissues (cerebrum, cerebellum, and kidney), and GAPDH was stably expressed in four tissues (cerebrum, ventricle, psoas muscle, and kidney). In comparison, GYS1, TBP, and ACTB were found to have CV values over 10% in all tissues. Of the seven genes examined, four (HPRT1, PPIA, YWHAZ, and GAPDH) were found to be stably expressed across multiple organs, with low CV values (< or =10%). CONCLUSIONS: These results will provide fundamental information regarding internal controls for protein expression studies and can be used for analysis of postmortem protein degradation patterns in forensic medicine.
Animals ; Blotting, Western ; Cerebellum ; Forensic Medicine ; Genes, Essential* ; Heart Ventricles ; Kidney ; Liver ; Postmortem Changes ; Proteolysis ; Psoas Muscles ; Rats* ; Spleen