We have previously observed that a sequence in coat protein (CP) ORF of Turnip yellow mosaic virus (TYMV) is required for efficient replication of the virus. The sequence was predicted to take a stem-loop structure, thus termed SL2. While examining various SL2 mutants, we observed that all the modifications resulting in extension of translation beyond the CP ORF significantly suppressed subgenomic RNA accumulation. The genomic RNA level, in contrast, was not affected. Introduction of an in-frame stop codon in the CP ORF of these constructs restored the level of subgenomic RNA. Overall, the results suggest that the read-through makes the subgenomic RNA unstable.
Animals ; Brassica napus ; Codon, Terminator ; Ecthyma, Contagious ; RNA ; Tymovirus ; Viruses

Nowadays, there are a lot of evidence that mutation of the p53 tumor suppressor gene is one of the most common genetic abnormalities in neoplastic progression. In this study, we analyzed 20 specimens of oral tumors (squamous cell carcinoma 14 cases, ameloblastoma 3 cases, adenoid cystic carcinoma 2 cases, malignant schwannoma 1 case) using polymerase chain reaction and direct sequencing which used an automated DNA sequencer and software for detection of mutations. Polymerase chain reactions were performed with 4 sets of primers encompassing exon 5, 6, 7, 8, and direct sequencing method was employed. The results were as followings. 1. We detected 10 piont mutations out of 20 specimens (50%). 2. The genetic alterations included 7 mis-sense mutations resulting in single amino acid subtitutions, 2 silent mutations, 1 non-sense mutations encoding a stop codon. 3. Mutations were mostly in exon 7(7 out of 10 mutations, 70%) and involved codons 225, 234, 235, 236, 238, 247. 4. Therse were 4 cases of T-->A transversion, 2 cases of C-->A transversion, A-->G transition, 1 case of C-->G, T-->G transversion respectively. 5. We could find out point mutations more conveniently using PCR-Automated Direct Sequencing method.
Ameloblastoma ; Carcinoma, Adenoid Cystic ; Codon ; Codon, Terminator ; DNA ; Exons ; Genes, p53 ; Genes, Tumor Suppressor* ; Neurilemmoma ; Point Mutation ; Polymerase Chain Reaction

The molecular defect of congenital lipoid adrenal hyperplasia has been discovered to be in the transport of cholesterol into mitochondria due to defective regulatory protein called "Steroidogenic Acute Regulatory Protein (StAR)", while the enzyme P450scc itself is normal. This study with EcoRII restriction enzyme aimed at elucidating more conveniently the molecular defect in the StAR gene. The genomic DNAs were extracted from their peripheral blood. We amplified the exon 7, hot spot, of the StAR gene with 1 set of primers by Polymerase Chain Reaction (PCR). Subsequently, a PCR product corresponding to target sequence (~437 bps) from the patient and her father have been sequenced by automatic sequence analyzer. The PCR-RFLP (Restriction Fragment Length Polymorphism) analysis after restriction digestion with EcoRII restriction enzyme was also performed on 12% polyacrylamide gel electrophoresis. The mutation was identified in the exon 7 of the StAR gene, substituting C for T at codon 258, consequently replacing glutamine by stop codon. This mutation alters EcoRII restriction site. In addition, we obtained the good result of PCR-RFLP (Restriction Fragment Length Polymorphism) analysis on 12% polyacrylamide gel electrophoresis. Therefore, the PCR-RFLP (Restriction Fragment Length Polymorphism) analysis with EcoRII restriction enzyme can be easily utilized to screen carrier, diagnose the patient prenatally or postnatally.
Cholesterol ; Codon ; Codon, Terminator ; Digestion ; DNA ; Electrophoresis, Polyacrylamide Gel ; Exons ; Fathers ; Glutamine ; Humans ; Hyperplasia ; Mitochondria ; Molecular Biology* ; Polymerase Chain Reaction

BACKGROUND: Angiogenin, a 14.1-kDa protein isolated from the medium conditioned by HT-29 human colon carcinoma cells, induces the angiogenesis. In contrast to the human angiogenin, thought to have one homologue, the mouse angiogenin is known to have several angiogenin homologues. During we were investigating the target genes, overexpressed by the chimeric PAX3/FKHR transcription factor, new gene closely similar to the mouse angiogenin rather than angiogenin itself was obtained. We report this Ang-vl gene to understand the process of angiogenesis by comparing the mouse angiogenin family genes. METHODS: The representational difference analysis was used to investigate the target genes over expressed by the PAX3/FKHR chimeric transcription factor. The target genes were subcloned into the pBluescriptSK + and sequenced using the 73 and 77 vector itself primers. Analyses of the completed consensus nucleic acid and peptide sequences were performed using the intelligenetics and GCG software packages as well as BLAST algorithms. RESULTS: The Ang-vl gene, including the glutamine that becomes the N-terminal amino acid by the post-translational peptidase reaction and stop codon, was obtained. CONCLUSIONS: We cloned the one member of the mouse angiogenin family genes. From the point of protein chemistry, the mechanism of angiogenin or, for that matter, of any other blood vessel inducing proteins is not yet known. However, the homologues of the angiogenin might interact each other to regulate the angiogenesls. In this regard, the Ang-vl gene provides an opportunity to understand the mechanism of angiogenesis.
Animals ; Blood Vessels ; Chemistry ; Clone Cells ; Codon, Terminator ; Colon ; Consensus ; Glutamine ; Humans ; Mice* ; Transcription Factors*

Pseudohypoparathyroidism type Ia (PHP Ia) is a disorder characterized by multiform hormonal resistance including parathyroid hormone (PTH) resistance and Albright hereditary osteodystrophy (AHO). It is caused by heterozygous inactivating mutations within the Gs alpha-encoding GNAS exons. A 9-year-old boy presented with clinical and laboratory abnormalities including hypocalcemia, hyperphosphatemia, PTH resistance, multihormone resistance and AHO (round face, short stature, obesity, brachydactyly and osteoma cutis) which were typical of PHP Ia. He had a history of repeated convulsive episodes that started from the age of 2 months. A cranial computed tomography scan showed bilateral calcifications in the basal ganglia and his intelligence quotient testing indicated mild mental retardation. Family history revealed that the patient's maternal relatives, including his grandmother and 2 of his mother's siblings, had features suggestive of AHO. Sequencing of the GNAS gene of the patient identified a heterozygous nonsense mutation within exon 11 (c.637 C>T). The C>T transversion results in an amino acid substitution from Gln to stop codon at codon 213 (p.Gln213*). To our knowledge, this is a novel mutation in GNAS.
Amino Acid Substitution ; Basal Ganglia ; Brachydactyly ; Child ; Codon ; Codon, Nonsense ; Codon, Terminator ; Exons ; Humans ; Hyperphosphatemia ; Hypocalcemia ; Intellectual Disability ; Intelligence ; Male ; Obesity ; Osteoma ; Parathyroid Hormone ; Pseudohypoparathyroidism* ; Siblings

In order to understand the role of mec regulator genes in the evolution of methicillin-resistant S. aureus (MRSA), the distribution of the mec regulator genes among the 66 clinical isolates of MRSA was analysed. And also the correlation between gene mutation and degree of phenotypic expression of resistance was studied. Fifty strains carried whole mec regulator region, while the mecI gene and nearly half of the 3'-end of the mecR#l gene were deleted in fifteen strains. The mecRl MS gene was detected among all of the mecA carried strains, but the mecRl PB gene was carried by 77% of the MRSA strains. At least a portion of the 5'-end region of the mecRl gene was carried by all MRSA strains tested. Forty-seven strains were finally confirmed to have mecI gene and each mecI gene of above strains was sequenced for identification of the relationship between repressor function of mecI gene on mecA transcription and MIC level of methicillin. Point mutations were detected in 11 strains of 47 strains. In 8 strains, there was one nucleotide substitution (C to T at position 202) that produced a new termination codon at position 201. In 3 strains, one nucleotide substitution from G to T at position 43 caused an amino acid substitution from Val to Phe. The MIC of methicillin of strains carrying mutated mecI genes ranged 256 ug/ ml to 1024 ug/ml. Transcription level of amplified cDNA corresponding to mecA was determined by the method of RT-PCR of extracted RNA. Total RNA was extracted from two strains with mutated mecI gene and a strain with intact mecI gene. Deletional loss or the mutational inactivation of the mecI gene did not affect the level of mecA transcription. Role of mecI gene as a strong repressor function on mecA gene seemed to be skeptical.
Amino Acid Substitution ; Codon, Terminator ; DNA, Complementary ; Genes, Regulator* ; Methicillin Resistance ; Methicillin* ; Methicillin-Resistant Staphylococcus aureus ; Point Mutation ; RNA

APOBEC-1 Deaminase ; genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; Codon, Terminator ; Gene Editing ; methods ; Humans ; Zygote ; beta-Globins ; genetics

Cornelia de Lange Syndrome (CdLS) is a multiple congenital anomaly characterized by distinctive facial features, upper limb malformations, growth and cognitive retardation. The diagnosis of the syndrome is based on the distinctive clinical features. The etiology is still not clear. Mutations in the sister chromatid cohesion factor genes NIPBL, SMC1A (also called SMC1L1) and SMC3 have been suggested as probable cause of this syndrome. We experienced a case of newborn with CdLS showing bushy eyebrows and synophrys, long curly eyelashes, long philtrum, downturned angles of the mouth and thin upper lips, cleft palate, micrognathia, excessive body hair, micromelia of both hands, flexion contracture of elbows and hypertonicity. We detected a NIPBL gene mutation in a present neonate with CdLS, the first report in Korea.
Codon, Nonsense ; Codon, Terminator ; De Lange Syndrome/diagnosis/*genetics/ultrasonography ; Heterozygote ; Humans ; Infant, Newborn ; Male ; Proteins/*genetics ; Sequence Analysis, DNA ; Tomography, X-Ray Computed

Toxascaris leonina is a common parasitic nematode of wild mammals and has significant impacts on the protection of rare wild animals. To analyze population genetic characteristics of T. leonina from South China tiger, its mitochondrial (mt) genome was sequenced. Its complete circular mt genome was 14,277 bp in length, including 12 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions. The nucleotide composition was biased toward A and T. The most common start codon and stop codon were TTG and TAG, and 4 genes ended with an incomplete stop codon. There were 13 intergenic regions ranging 1 to 10 bp in size. Phylogenetically, T. leonina from a South China tiger was close to canine T. leonina. This study reports for the first time a complete mt genome sequence of T. leonina from the South China tiger, and provides a scientific basis for studying the genetic diversity of nematodes between different hosts.
Animals ; Animals, Wild ; Bias (Epidemiology) ; China* ; Codon, Initiator ; Codon, Terminator ; DNA, Intergenic ; Genes, rRNA ; Genetic Variation ; Genome ; Genome, Mitochondrial* ; Mammals ; Phylogeny ; RNA, Transfer ; Sequence Analysis* ; Tigers* ; Toxascaris*

To define the genes for production of catalytically active H. pylori urease, we camed out study to elucidate the structure of urease gene transcript, to delineate the genetic region which affected the extent of the expression and the activation of urease structural subunits. UreC and ureD were confirmed not to affect the expression of structural genes and active enzyme production, meaning that these genes are not components of the urease gene cluster of H. pylori. p-independent transcriptional stop signal was found in 12 bp down-stream of ureH stop codon. RNA extension test showed that the transcript starts with 267 bp upstream of ureA start codon. Although accessory genes did not affect the extent of the expression of the structural subunits, they were essential for assembling the active urease in E. coli. E. coli transformants of plasmid clones containing ureAB produced catalytically active urease when they are complemented with the plasmid clones of ureIEFGH or coexisted with ureIEFGH, meaning that accessory gene products could be trans-acting as well as cis-acting. The extent of production of urease structural subunits depended on the region of 241 to 57 bp upstream of ureA start codon. E. coli transformant of pBeloBACII clone containing the urease gene cluster, which is maintained with a single copy in host, did not express the urease. Proteins (60, 38, 30, 29, 27, and 24 kDa) that could hold nickel ions were identified in the cell extract of H. pylori. The results in this study will provide the basis to understand the control mechanism for urease gene expression and formation of the active urease.
Clone Cells ; Codon, Initiator ; Codon, Terminator ; Complement System Proteins ; Gene Expression ; Helicobacter pylori* ; Helicobacter* ; Ions ; Multigene Family ; Nickel ; Plasmids ; RNA ; Urea ; Urease*