There have been attempts to use consensus sequences or ancestor sequences for development vaccines against viruses with high diversity and variation. In this study, we generated and compared consensus sequences and ancestor sequences of nef and vif genes of HIV-1 isolated from Koreans. Phylogenetic analyses revealed that majorities of the Korean isolates were clustered to form the Korean clade within subtype B (KcB) where foreign isolates were not included. Consensus sequences inferred from the KcB as well as from all Korean isolates were almost identical but significantly different from subtype B consensus sequence or HIV-1 consensus sequence. The genetic distances from one of the Korean isolates to the other Korean isolates were much longer than to the consensus or ancestor sequences deduced from Korean isolates but similar to those of subtype B or HIV-1. Moreover, the genetic distances from the Korean isolates to the consensus sequences were shorter than to the ancestor sequences both in nef and vif genes. Thus, the consensus sequences may be useful in developing Korean-specific HIV-1 vaccine.
Consensus Sequence* ; Consensus* ; Genes, vif* ; HIV-1* ; Vaccines

The three components of taxonomy are classification, nomenclature and identification. Traditionally, bacterial classification and identification were performed based on the morphology and the biochemical data of the bacteria. In newer theories, or so-called natural concepts, the relationships between bacteria are based on the overall similarities of both the phenotypic and genotypic characteristics. The polyphasic taxonomy, or current taxonomy, describes the integration of all of the available genotypic, phenotypic, and phylogenetic information into a consensus type of general-purpose classification. When routine identification methods that are based on the biochemical tests fail, alternative procedures such as complete 16s rRNA gene sequence analysis are required. Although the results of 16s rRNA gene sequence analysis have not been fully discriminatory to differentiate closely related species, they may guide the additional analyses that are required for species identification.
Bacteria ; Consensus ; Genes, rRNA ; Sequence Analysis

Gene mutation (e.g. substitution, insertion and deletion) and related phenotype information are important biomedical knowledge. Many biomedical databases (e.g. OMIM) incorporate such data. However, few studies have examined the quality of this data. In the current study, we examined the quality of protein single-point mutations in the OMIM and identified whether the corresponding reference sequences align with the mutation positions. Our results show that close to 20% of mutation data cannot be mapped to a single reference sequence. The failed mappings are caused by position conflict, site shifting (peptide, N-terminal methionine) and other types of data error. We propose a preliminary model to resolve such inconsistency in the OMIM database.
Amino Acid Sequence ; Consensus Sequence ; Databases, Genetic ; Molecular Sequence Data ; Point Mutation ; Sequence Alignment

The nucleotide sequence of pZMO1, a small cryptic plasmid of Zymomonas mobilis ATCC10988 was determined. Analysis of 1,680 bp of sequence revealed 69% identity with Shigella sonnei plasmid, pKYM and 61% identity with Nostoc sp. ss DNA replicating plasmid. Analysis of a deduced amino acid sequence of an orf of pZMO1 revealed 75% identity and 90% similarity with the repA gene of Synechocystis sp. plasmid pCA2.4. The upstream region of the repA gene of pZMO1 possesses six directed repeat sequences and two inverted repeat sequences at downstream of the IR consensus sequence of nick region of rolling circle replication (RCR) plasmid. A typical terminator hairpin structure was found at the downstream region of repA gene. Degradation of single-stranded plasmid DNA by S1 nuclease was detected by Southern hybridization. It suggests that pZMO1 replicates by a rolling circle mechanism in Z. mobilis ATCC10988 cells.
Amino Acid Sequence ; Animals ; Base Sequence ; Consensus Sequence ; DNA ; Ecthyma, Contagious ; Inverted Repeat Sequences ; Nostoc ; Plasmids* ; Shigella sonnei ; Synechocystis ; Zymomonas*

Ancient bones have undergone natural decomposition and have been exposed to external environment for long period. Ancient DNA from old bone is usually fragmented. In addition, various kinds of inhibitors are co-extracted. All these may inhibit proper sequencing reaction. Cloning is regarded as the standard method when sequencing aDNA. When cloning, each clone from the same sample may not be of same sequence, and to exact consensus sequence may be difficult. Here we present our experience on 1200 year old bone from Russia, Primorsky Kray area. We have tried to sequence for HV I, II region of mtDNA using modified mini-primer set, which consisted of 7 set to cover the HV I, II. We cloned the PCR product and sequenced all the clones. Amplification efficiency and subsequent success rates were different for each mini primer set. Loci of variation that differ from consensus sequences were rather frequent, and the pattern were variable depending on sample. Except major polymorphic sites that are important when haplogroup designation, 16129 was the most frequent site that was discarded when extracting haplogroup designation.
Clone Cells ; Cloning, Organism ; Consensus Sequence ; DNA ; DNA, Mitochondrial ; Polymerase Chain Reaction ; Russia

A 37-year-old female was presented with an epidermal cyst on her lower back. Histopathologic examination was consistent with an epidermoid cyst with seborrheic verrucalike cyst wall and acantholytic change was also found in the cyst wall. Human papillomavirus(HPV)-specific DNA sequences in paraffin-embedded tissue section were not detected by polymerase chain reaction using HPV consensus primers.
Acantholysis* ; Adult ; Base Sequence ; Consensus ; Epidermal Cyst* ; Female ; Humans ; Polymerase Chain Reaction

Over the last two decades, the systemic treatment of cancer has evolved from cytotoxic chemotherapy to targeted therapy and now immunotherapy. Next-generation sequencing (NGS) is entering clinical applications for cancer treatment through the help of more powerful computational analyses. The increasing number of targeted therapies approved by regulatory authorities (RAs) with or without biomarkers necessitates the screening of multiple biomarkers using NGS, which is now approved and reimbursed by Korean RAs for some types of malignancies. However, the clinical utility of NGS remains to be established as a prerequisite for its routine incorporation into clinical practice. Currently, the best scenario of NGS use in clinics is to enroll patients into clinical trials based on the detection of biomarkers, but this is only possible in the hospitals conducting the specific trial. The other scenario is the off-label use of a targeted drug, but this requires social consensus for future implementation. The clinical applications of NGS are expanding in terms of its platforms, from targeted sequencing to whole exome and RNA sequencing, and in terms of systemic therapy, from targeted therapy to immunotherapy. Research into tumor mutational burden and neoantigens is shedding new light on the clinical use of NGS in immunotherapy.
Biomarkers ; Consensus ; Drug Therapy ; Exome ; Humans ; Immunotherapy ; Mass Screening ; Off-Label Use ; Sequence Analysis, RNA

Animals ; Base Pairing ; Binding Sites ; CCCTC-Binding Factor ; metabolism ; Consensus Sequence ; Humans ; Mutation ; Nucleotide Motifs

BACKGROUND: The role of the interferon consensus sequence binding protein (ICSBP), a member of interferon regulatory factor family, in protecting against a vesicular stomatitis virus (VSV) infection has not been firmly elucidated. Thus, it was investigated utilizing the human promyelocytic leukemia HL-60 cells which do not express ICSBP. METHODS: HL-60 cells were stably transfected with plasmid containing cDNA for either ICSBP or DNA binding domain (DBD) and tested for their VSV-susceptibilities. The susceptibility of each transfectant group to a VSV infection was determined by a plaque assay at 1 h, 24 h, and 48 h post-infection in the presence (500 IU/ml) or absence of interferon alpha(IFN alpha). RESULTS: In the absence of IFN alpha, the three groups showed similar sensitivities to a VSV infection. However, when pre-treated with IFN, the viral titers in both the ICSBP and control clones steadily decreased over 48 h of incubation, indicating the existence of IFN alpha-mediated protection against VSV infection. The IFN alpha-treated ICSBP clones appeared to be more resistant to infection compared with the control clones, although the difference was not great . On the contrary, the viral titers in the IFN alpha-treated DBD clones increased at 24 h then decreased by 48 h. CONCLUSION: The expression of truncated ICSBP (DBD) does not appear to underlie the impaired protection against a VSV infection in the DBD clones, since even the control clones lacking ICSBP were protected from a VSV infection. This suggests that ICSBP does not play a critical role in the IFN alpha-mediated anti-VSV response of HL-60 cells, although it appears to confer some resistance to a VSV infection.
Carrier Proteins* ; Clone Cells ; Consensus Sequence* ; Consensus* ; DNA ; DNA, Complementary ; HL-60 Cells* ; Humans ; Interferon-alpha ; Interferons* ; Leukemia ; Plasmids ; Vesicular Stomatitis

We investigated whether the two variant elements of CRE(TGcCGTCA[5'CRE], TGACcTCA[3'CRE]) in the 5'flanking region of the rat TRH gene, which are different from the CRE consensus sequence(5'-TGACGTCA-3') by one base pair, are responsive to cAMP, and whether the one base pair difference is responsible for the degree of cAMP responsiveness of the gene. When CA 77 cells were stimulated with forskolin and isobutylmethylxanthine for 4 hours, the level of TRH mRNA was increased by only two fold. The transient gene expression study using serial 5'deletion of the TRH gene in PC12 cells showed that the region between-113 and-77, which includes 5'CRE, was crucial for the cAMP resonsiveness. When the plasmid, which contains the 30 bp oligonucleotide including either 5'CRE or 3'CRE ligated to the enhancerless RSV promoter, was transfected into PC12 cells, it did not significantly affect not only the basal transcription but cAMP responsiveness. The 65 bp oligonucleotide including both 5'CRE and 3'CRE, however, increased both of the basal transcription and cAMP-stimulated transcription by 2-3 fold. When the sequence of 5'CRE was converted to that of the CRE consensus by replacing one base pair, the cAMP responsiveness was increased by two fold although the basal transcription was not increased. The one base pair mutant of 3'CRE increased both of the basal and cAMP-stimulated transcription by 3-4 fold. These results suggest that there are the two variant CREs in rat TRH gene, which are relatively weak CRE compared to the CREs of other neuropeptide genes and cooperative for the activation of both the basal and cAMP-stimulated transcription. The one base pair difference of the variant CREs from the CRE consensus sequence is responsible for the weak responsiveness to cAMP.
Animals ; Base Pairing ; Colforsin ; Consensus ; Consensus Sequence ; Cyclic AMP ; Gene Expression ; Neuropeptides ; PC12 Cells ; Plasmids ; Rats ; Response Elements ; RNA, Messenger ; Thyrotropin ; Thyrotropin-Releasing Hormone