BACKGROUND: Examining the biological susceptibility of Mycobacterium tuberculosis to pyrazinamide (PZA) in vitro is very difficult as PZA is inactive under normal culture conditions. The susceptibility test, an enzyme assay for Pzase activity, and a genetic test for pncA gene mutations, were performed in order to predict PZA resistance. METHODS: 28 cultured clinical isolates of Mycobacterium tuberculosis were tested. The biological susceptibility was performed by the absolute concentration method using Lowenstein-Jensen media. The PZase activity was tested by means of Wayne's method. A 710-bp region includes the entire open reading frame of pncA was amplified and sequenced. RESULTS: All six strains with positive PZase activity exhibited no pncA mutations with one strain showing a false resistance in the biological susceptibility test. Among the 22 strains with no PZase activity, 21 exhibited showed pncA mutations. In the biological suscaptibility test, 20 strains were resistant, and one was susceptible, and the other failed to test. The mutation types varied with ten missense, one silent and one nonsense mutation 1 slipped-strand mispairing, and 6 frameshift mutations. Three strains had an adenine to guanine mutation at position - 11 upstream of the start codon. CONCLUSION: The mutation at the pncA promotor region is frequent at -11 upstream position. Automatic sequencing of pncA is a useful tool for rapid and accurate detection of PZA resistant M.tuberculosis, and for demonstrating the epidemiological relatedness of the PZA-resistant M.tubersulosis strains.
Adenine ; Codon, Initiator ; Codon, Nonsense ; Enzyme Assays ; Frameshift Mutation ; Guanine ; Mycobacterium tuberculosis* ; Mycobacterium* ; Open Reading Frames ; Promoter Regions, Genetic ; Pyrazinamide*

By altering the electrostatic charge of histones or providing binding sites to protein recognition molecules, Chromatin marks have been proposed to regulate gene expression, a property that has motivated researchers to link these marks to cis-regulatory elements. With the help of next generation sequencing technologies, we can now correlate one specific chromatin mark with regulatory elements (e.g. enhancers or promoters) and also build tools, such as hidden Markov models, to gain insight into mark combinations. However, hidden Markov models have limitation for their character of generative models and assume that a current observation depends only on a current hidden state in the chain. Here, we employed two graphical probabilistic models, namely the linear conditional random field model and multivariate hidden Markov model, to mark gene regions with different states based on recurrent and spatially coherent character of these eight marks. Both models revealed chromatin states that may correspond to enhancers and promoters, transcribed regions, transcriptional elongation, and low-signal regions. We also found that the linear conditional random field model was more effective than the hidden Markov model in recognizing regulatory elements, such as promoter-, enhancer-, and transcriptional elongation-associated regions, which gives us a better choice.
Binding Sites ; Chromatin ; genetics ; Enhancer Elements, Genetic ; Epigenomics ; Histones ; genetics ; Humans ; Markov Chains ; Models, Genetic ; Models, Statistical ; Promoter Regions, Genetic ; Regulatory Elements, Transcriptional

The self-splicing group I intron from Tetrahymena thermophila has been demonstrated to perform splicing reaction with its substrate RNA in the trans configuration. In this study, we explored the potential use of the trans-splicing group I ribozymes to replace a specific RNA with a new RNA that exerts any new function we want to introduce. We have chosen thymidine phosphorylase (TP) RNA as a target RNA that is known as a valid cancer prognostic factor. Cancer-specific expression of TP RNA was first evaluated with RT-PCR analysis of RNA from patients with gastric cancer. We determined next which regions of the TP RNA are accessible to ribozymes by employing an RNA mapping strategy, and found that the leader sequences upstream of the AUG start codon appeared to be particularly accessible. A specific ribozyme recognizing the most accessible sequence in the TP RNA with firefly luciferase transcript as a 3' exon was then developed. The specific trans-splicing ribozyme transferred an intended 3' exon tag sequence onto the targeted TP transcripts, resulting in a more than two fold induction of the reporter activity in the presence of TP RNA in mammalian cells, compared to the absence of the target RNA. These results suggest that the Tetrahymena ribozyme can be a potent anti-cancer agent to modify TP RNAs in tumors with a new RNA harboring anti-cancer activity.
Codon, Initiator ; Exons ; Fireflies ; Humans ; Introns ; Luciferases ; RNA* ; RNA, Catalytic ; Stomach Neoplasms ; Tetrahymena ; Tetrahymena thermophila ; Thymidine Phosphorylase ; Trans-Splicing*

The DNA sequence of a plasmid named pHP489 of Helicobacter pylori strain 489 was determined and analyzed to characterize its replication apparatus. The pHP489 plasmid consisted of 1,222 bp and had an overall G+C content of 33.1%. An ORF was predicted to encode the putative protein of 239 amino acid residues (28 kDa). A putative ribosomal binding site and a potential terminator sequence are located upstream and downstream of the ORF, respectively. However, the consensus sequence for a promoter in upstream of ORF was not found. A potential dna A box was found at 317 nt upstream of a start codon and followed by two-57 bp directed repeats and an inverted repeat. The DNA homology was found in the regions of less than 90 bp among pHPK255, pHPM180, and pHel1 of other H. pylori plasmids and Mycoplasma mycoides plasmids. pHP489K that was produced by pHP489 sequence and C. jejuni derived aph(3')-III, was transformed to various H. pylori isolates and were stably maintained in the H. pylori host without the addition of selective antibiotics for the 30-times subcultues. The plasmic vector, in which the ORF region of pHP489 DNA was deleted, could be transformed into H. pylori. However, the plasmid vector, whose the direct repeats region of pHP489 DNA was deleted, failed to be transformed. The direct repeats region of pHP489 DNA was confirmed to be bound with cytosolic factors of H. pylori. These results showed that the direct repeats region of pHP489 DNA is an essential apparatus by which the plasmid could be replicacted in H. pylori. And pHP489 plasmid was supposed to be replicated by host factors rather than plasmic-encoded factors.
Animals ; Anti-Bacterial Agents ; Base Composition ; Base Sequence ; Binding Sites ; Codon, Initiator ; Consensus Sequence ; Cytosol ; DNA ; Ecthyma, Contagious ; Helicobacter pylori* ; Helicobacter* ; Mycoplasma mycoides ; Plasmids* ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis* ; Terminator Regions, Genetic

OBJECTIVETo explore the clinical features and gene mutation profiles of patients with chronic hepatitis B (CHB) and Gilbert's syndrome.

METHODSThirty-three patients with CHB and Gilbert's syndrome were enrolled in the study. Serum markers of liver function and histological features of disease-related liver injury were assessed by standard methods. Gene mutations were detected by PCR and direct DNA sequencing.Statistical analysis was carried out with the chi-square and t tests.

RESULTSSequencing of the Gilbert syndrome-associated gene, UGT 1A 1, revealed mutations in the upstream promoter phenobarbital-responsive element module (PBREM) (-3279 mutation, 23 cases), in the promoter TATA box (a TA insertion mutation, 21 cases), and in the coding region of exon 1 (a GGA-AGA Gly71Arg mutation, 18 cases); there was no statistical difference found for any of the three mutations among this patient population (x2 =1.640, P more than 0.05).

CONCLUSIONThe traditional methods of diagnosis for patients with CHB and Gilbert's syndrome remain a technical challenge in the clinic, and gene detection may represent a more favorable method for diagnosing this patient population.

Base Sequence ; Exons ; Gilbert Disease ; Glucuronosyltransferase ; Hepatitis B, Chronic ; Humans ; Mutagenesis, Insertional ; Mutation ; Polymerase Chain Reaction ; Promoter Regions, Genetic ; TATA Box

IL-32 exists as seven mRNA transcripts that can translate into distinct individual IL-32 variants with specific protein domains. These translated protein domains of IL-32 variants code for specific functions that allow for interaction with different molecules intracellularly or extracellularly. The longest variant is IL-32γ possessing 234 amino acid residues with all 11 protein domains, while the shortest variant is IL-32α possessing 131 amino acid residues with three of the protein domains. The first domain exists in 6 variants except IL-32δ variant, which has a distinct translation initiation codon due to mRNA splicing. The last eleventh domain is common domain for all seven IL-32 variants. Numerous studies in different fields, such as inflammation, autoimmunity, pathogen infection, and cancer biology, have claimed the specific biological activity of individual IL-32 variant despite the absence of sufficient data. There are 4 additional IL-32 variants without proper transcripts. In this review, the structural characteristics of seven IL-32 transcripts are described based on the specific protein domains.
Autoimmunity ; Biology ; Codon, Initiator ; Inflammation ; Protein Structure, Tertiary ; RNA, Messenger

The main purpose of the this study was to find the candidate cis-elements in negative regulation region throngh analysing the DNA sequences of lrp16 gene promoter so as to provide the experimental basis for screening drugs with inhibitory effect on lrp16 gene expression. The open reading frame (ORF) sequences in uncoding DNA and mRNA sequences of 5' flanking region in lrp16 gene were cloned by the data in GeneBank and Internet; the possibly existing cis-element in thsi region was searched in databank of human transcriptional factor by using TESS and Genomax online promoter analysis software; the drugs related to inhibition of lrp16 gene expression were screened by using SAGE and GEO databank. The results showed that there were many cis-elements in the negative regulation region, including T-Ag, PU.1, c-Ets, XPF-1, P2 alphaA, IL6-6RE and RAR. In cultured cell lines, hormone or its inhibitor such as corticosteroid, tamoxifen, forskolin, phenylephrine, inflammatory factors such as IFNgamma and TNFalpha, and chemotherapeutics 5-fluorouracil could down-regulate the lrp16 gene expression as compared with absent ones. It is concluded that cis-elements including T-Ag, PU.1, c-Ets, XPF-1, P2 alphaA, IL6-6RE and RAR may inhibit lrp16 expression and hormone or its inhibitor such as corticosteroid, tamoxifen, forskolin, phenylephrine, inflammatory factors such as IL6, IFNgamma and TNFalpha, and chemotherapeutics 5-fluorouracil may participate in the regulation of lrp16 gene expression in negative manner.
Cell Line ; Computational Biology ; Gene Expression Regulation ; Humans ; Neoplasm Proteins ; drug effects ; genetics ; Open Reading Frames ; Regulatory Elements, Transcriptional

Placenta specific 8 (PLAC8, also known as ONZIN) is a multi-functional protein that is highly expressed in the intestine, lung, spleen, and innate immune cells, and is involved in various diseases, including cancers, obesity, and innate immune deficiency. Here, we generated a Plac8 knockout mouse using the CRISPR/Cas9 system. The Cas9 mRNA and two single guide RNAs targeting a region near the translation start codon at Plac8 exon 2 were microinjected into mouse zygotes. This successfully eliminated the conventional translation start site, as confirmed by Sanger sequencing and PCR genotyping analysis. Unlike the previous Plac8 deficient models displaying increased adipose tissue and body weights, our male Plac8 knockout mice showed rather lower body weight than sex-matched littermate controls, though the only difference between these two mouse models is genetic context. Differently from the previously constructed embryonic stem cell-derived Plac8 knockout mouse that contains a neomycin resistance cassette, this knockout mouse model is free from a negative selection marker or other external insertions, which will be useful in future studies aimed at elucidating the multi-functional and physiological roles of PLAC8 in various diseases, without interference from exogenous foreign DNA.
Adipose Tissue ; Animals ; Body Weight ; Codon, Initiator ; DNA ; Exons ; Humans ; Intestines ; Lung ; Male ; Mice ; Mice, Knockout* ; Neomycin ; Obesity ; Placenta ; Polymerase Chain Reaction ; RNA, Guide ; RNA, Messenger ; Spleen ; Zygote

Using overlapping and mutant oligonucleotides as probes, gel mobility assays and competition experiments identified a sequence from -47 to -32 bp upstream of the LIM2 CAP site, which a lens protein complex bound with high affinity which appeared to bind only to the "sense" strand of the double-stranded DNA molecule. This sequence consisted of a string of four guanine residues followed by seven other nucleotides (AACCTAA) and followed by another four guanines, i.e. GGGGAACCTAAGGGG, called the Hsu element. Promoter-CAT constructs containing this sequence or mutations of the sequence indicated that the Hsu element is located within the basal promoter, and is essential for expression of the LIM2 gene. The trans factors binding to the Hsu element are present throughout development, and appear to be lens-specific. Since the LIM2 gene promoter does not contain a classic TATA box, the Hsu element may serve as the site for binding the RNA polymerase complex.
Base Sequence ; Eye Proteins ; genetics ; Humans ; Membrane Proteins ; Molecular Sequence Data ; Promoter Regions, Genetic ; TATA Box

To characterize the molecular nature of human immunodeficiency virus (HIV)-1, we determined the full-length HIV-1 sequences from cultured peripheral blood mononuclear cells (PBMC) of a Korean long-term nonprogressor (LTNP). Without antiretroviral therapy, the individual has maintained CD4+ T counts over 500/microliter from 1989 to 1999. Plasma viral RNA copy was 992 U/ml in 1998. Culture supernatant showed positive from culture days 9.4 series of 9 overlapping PCR products were amplified from cultured PBMC and cloned. About 9.2 kb from R of 5' LTR to R of 3' LTR was determined by automated sequencing. The G-to-A hypermutations were shown throughout the entire region. As a result of G to A hypermutations, premature stop codon was found in integrase coding region. Though there was no recombination between subtypes over all genomes, TATA box in both LTRs was TAAAA which is detected in subtype E instead of TATAA in subtype B. And, there were nucleotide GC insertion between NF- kappaB I and Spl III, and duplication of TCF-lalpha in LTR. We could not find any deletion of amino acid in Nef, Gog, Pol and Euv gene. This study is the first report on molecular nature of full genomes of HIV-1 isolated in Korea.
Clinical Coding ; Clone Cells ; Codon, Nonsense ; Genome ; HIV ; HIV-1* ; Integrases ; Korea ; Plasma ; Polymerase Chain Reaction ; Recombination, Genetic ; RNA, Viral ; TATA Box