Human cytomegalovirus (HCMV) is a ubiquitous human pathogen and contains double stranded DNA genome with approximately 230 kbp. Molecular genomic studies of HCMV have been attempted in order to understand the pathogenesis and evolution of HCMV. However, studies on HCMV strains of Asian origin are limited. In this study, it was attempted to understand the genomics of HCMV isolated from Korea. Clinical strain LCW isolated from Korean patient was passaged in vitro cell culture, and subjected to next-generation sequencing. Complete genome sequence was obtained and compared with other HCMV strains. The LCW genome was found to contain 170 open reading frames (ORFs) and two ORF (RL5A and RL13) of the strain LCW were found to be truncated due to early stop codon. Phylogenetic analysis suggested that the strain LCW was closely related with Asian strains such as HCMV strains JHC and HAN. Common nucleotide sequences among the 3 Asian strains distinguishable from other strains were detected at 197 sites including 104 sites in ORFs.
Animals ; Asian Continental Ancestry Group ; Base Sequence ; Cell Culture Techniques ; Codon, Terminator ; Cytomegalovirus* ; DNA ; Ecthyma, Contagious ; Genome* ; Genomics ; Humans* ; In Vitro Techniques ; Korea ; Open Reading Frames

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

Familial adenomatous polyposis (FAP) is a precancerous clinical entity, which is characterized by the development of numerous adenomatous polyps throughout the colon and rectum. The majority of FAP are associated with mutations of the adenomatous polyposis coli (APC) gene. Until now, more than 1,000 different APC mutations have been reported and some mutations express attenuated phenotypes which are milder forms with 10~100 colorectal polyps. We identified a novel mutation of APC gene which expressed an attenuated FAP but caused large gastroduodenal tubular adenomas requiring repeated endoscopic resections. A 16-year-old girl was referred to Incheon St. Mary's Hospital for evaluation of gastric polyposis. Initial esophagogastroduodenoscopy (EGD) showed numerous gastric polyps in the fundus and upper body and a few polyps in the duodenum. Pathologic examination confirmed gastric polyps as fundic gland polyps and duodenal polyps as tubular adenomas. Only a few colonic polyps of 2 to 5 mm in size were found on colonoscopy. Genetic analysis using polymerase chain reaction and direct sequencing revealed a novel stop codon mutation at codon 1522 in exon 16 of APC gene. At 12-month, 18-month, and 35-month follow-up EGD, large duodenal polyp and gastric polyps were removed endoscopically.
Adenoma ; Adenomatous Polyposis Coli* ; Adenomatous Polyps ; Adolescent ; Codon ; Codon, Terminator ; Colon ; Colonic Polyps ; Colonoscopy ; Duodenum ; Endoscopy, Digestive System ; Exons ; Female ; Follow-Up Studies ; Genes, APC* ; Germ-Line Mutation* ; Humans ; Incheon ; Phenotype ; Polymerase Chain Reaction ; Polyps* ; Rectum

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*

Protein S (PS), a vitamin K-dependent glycoprotein, performs an important role in the anticoagulation cascade as a cofactor of protein C. Because of the presence of a pseudogene and two different forms of PS in the plasma, protein S deficiency (PSD) is one of the most difficult thrombophilias to study and a rare blood disorder associated with an increased risk of thrombosis. We describe a unusual case of previously healthy 37-year-old man diagnosed with portal-splenic-mesenteric vein thrombosis secondary to PSD. The patient was admitted to the hospital due to continuous nonspecific abdominal pain and nausea. Abdominal computed tomography revealed acute venous thrombosis from inferior mesenteric vein to left portal vein via splenic vein, and laboratory test revealed decreased PS antigen level and PS functional activity. Conventional polymerase chain reaction and direct DNA sequencing analysis of the PROS1 gene demonstrated duplication of the 166th base in exon 2 resulting in frame-shift mutation (p.Arg56Lysfs*10) which is the first description of the new PROS1 gene mutation to our knowledge. Results from other studies suggest that the inherited PSD due to a PROS1 gene mutation may cause venous thrombosis in a healthy young man without any known predisposing factor.
Adult ; Anticoagulants/therapeutic use ; Base Sequence ; Blood Proteins/*genetics ; Codon, Terminator ; Exons ; Humans ; Male ; Mesenteric Veins/radiography ; Polymorphism, Restriction Fragment Length ; Portal Vein/radiography ; Protein S Deficiency/complications/*diagnosis ; Sequence Analysis, DNA ; Splenic Vein/radiography ; Tomography, X-Ray Computed ; Venous Thrombosis/*diagnosis/drug therapy/etiology

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

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

Attenuated familial adenomatous polyposis (AFAP) is a variant of familial adenomatous polyposis with fewer than one hundred colorectal polyps and a later age of onset of the cancer. Here, we report two cases of AFAP within family members. Each patient demonstrated the same novel germ line mutation in exon 15 of the adenomatous polyposis coli (APC) gene and was successfully managed with sulindac after refusal to perform colectomy: a 23-year-old man with incidentally diagnosed gastric adenoma and fundic gland polyps underwent colonoscopy, and fewer than 100 colorectal polyps were found; a 48-year-old woman who happened to be the mother of the 23-year-old man also showed fewer than 100 colorectal polyps on colonoscopy. Genetic analysis revealed a novel frameshift mutation in exon 15 of the APC gene. The deletion of adenine-guanine with the insertion of thymine in c.3833-3834 resulted in the formation of stop codon 1,287 in both patients. The patients were treated with sulindac due to their refusal to undergo colectomy. The annual follow-up upper endoscopy and colonoscopy in the following 2 years revealed significant regression of the colorectal polyps in both patients.
Adenoma ; Adenomatous Polyposis Coli ; Age of Onset ; Codon, Terminator ; Colectomy ; Colonoscopy ; Disulfiram ; Endoscopy ; Exons ; Female ; Follow-Up Studies ; Frameshift Mutation ; Genes, APC ; Germ-Line Mutation ; Humans ; Mothers ; Polyps ; Sulindac ; Thymine

BACKGROUND/AIMS: Gastrointestinal stromal tumors (GISTs) strongly express a receptor tyrosine kinase (RTK, c-KIT-CD117) harboring a KIT mutation that causes constitutive receptor activation leading to the development and growth of tumors; 35% of GISTs without KIT mutations have platelet-derived growth factor receptor alpha (PDGFRA) mutations, and the type of mutation plays an important role in the response to treatment. This study aimed to establish the frequency of stop codon mutations in the RTKs, KIT, and PDGFRA, in GISTs and correlate this molecular alteration with protein expression and treatment responsiveness. METHODS: Seventy-nine GISTs were analyzed for both KIT and PDGFRA mutations. Immunohistochemical expression was studied in tissue microarray blocks. RESULTS: We found three rare KIT mutations in exon 11 that induced a stop codon, two at position 563 and one at position 589, which have never been described before. All three tumors were CD117-, DOG1-, and CD34-positive. Two patients with a KIT stop codon mutation did not respond to imatinib therapy and died shortly after treatment. CONCLUSIONS: The association between stop codon mutations in KIT and patient survival, if confirmed in a larger population, may be useful in choosing effective therapies.
Benzamides ; Codon, Terminator ; Exons ; Gastrointestinal Stromal Tumors ; Growth and Development ; Humans ; Piperazines ; Protein-Tyrosine Kinases ; Pyrimidines ; Receptor, Platelet-Derived Growth Factor alpha ; Receptors, Platelet-Derived Growth Factor

OBJECTIVETo analyze the full nucleotide sequence of a null allele of major histocompatibility complex class I chain-related gene (MICA).

METHODSA sequence-based typing method was used to determine the nucleotide sequence of the MICA gene. Potential alleles were identified with a computer program.

RESULTSThe identified allele has possessed a sequence similar to that of MICA*027 except for a C→T substitution at position 184 in codon 62 (CAG→TAG) of exon 2. As a stop codon, this may result in a truncated protein.

CONCLUSIONA null allele of MICA gene has been identified. The sequence has been submitted to the Genbank nucleotide sequence database (submission No. HWS10011131), which was officially named as MICA*063N by the WHO Nomenclature Committee in October 2010.

Alleles ; Base Sequence ; Codon, Terminator ; Exons ; Female ; Histocompatibility Antigens Class I ; genetics ; Humans ; Middle Aged ; Molecular Sequence Data ; Sequence Analysis ; methods