The aim of this study was to identify a new gene of Haemophilus parasuis that could be used to develop a polymerase chain reaction (PCR) test for this porcine pathogen. H. parasuis genomic DNA was cloned into a set of expression vectors, and transformants expressing His-tagged polypeptides were identified by colony blotting. An ABC transporter-like gene was isolated. The cloned DNA fragment is 1,105 base pair and shows 78% similarity at the nucleotide level with an ABC transporter gene of H. ducreyi. Based on this sequence, two PCR primers were designed to amplify the entire 1,105-bp fragment in the proposed diagnostic PCR test. PCR amplification was able to detect a minimum of 1 x 10(4) CFU/ml of H. parasuis organisms. Fifteen different H. parasuis serovars were positive using the PCR test. No amplification was observed when the test was done using DNA from 16 other bacterial species commonly isolated from swine.
Base Pairing ; Clone Cells ; Cloning, Organism ; DNA ; Haemophilus ; Haemophilus parasuis ; Peptides ; Polymerase Chain Reaction ; Swine

Base Pairing ; Dimerization ; Genome, Viral ; RNA, Viral ; chemistry ; genetics ; Retroviridae ; chemistry ; genetics

BACKGROUND AND OBJECTIVES: The ability to taste the bitter compounds phenylthiocarbamide is a classic inherited trait in humans. This trait has also been shown to correlate with a number of dietary preferences and thus may have important implications for human health. Recently, the PTC gene that underlies the phenotype was identified. Three single nucleotide polymorphisms in the PTC gene that result in three aminoacid substitutions (A49P, V262A, I296V) demonstrated a strong association with taster status in several studies. The aim of this study was to investigate the relationship between PTC genotype and taster status in normal volunteers. SUBJECTS AND METHOD: Seventy-three healthy normal volunteers were included. Phenylthiocarbamide detection threshold test was performed with successive solutions, which was comprised of a total of 15 grades. PTC gene haplotypes were defined by havingsingle nucleotide polymorphisms at the base pairs, 145,785 and 886, on the PTC gene. RESULTS: Taste sensitivity to phenylthiocarbamide had a bimodal distribution, which givesrise to the practice of dichotomizing subjects into 'tasters' and 'non-tasters'. The percentages of taster and non-taster were 80.8% and 19.2%, respectively. Haplotype analyses of the three single nucleotide polymorphisms inside the PTC gene allowed to identify only two haplotypes that were associated with the non-taster phenotype (100% AVI homozygous) and the taster phenotype (49% PAV homozygous and 51% PAV/AVI heterozygous). CONCLUSION: There was strong concordance between non-tasters defined by phenylthiocarbamide threshold and AVI homozygous by genotype in normal volunteers.
Base Pairing ; Factor IX ; Genotype ; Haplotypes ; Humans ; Phenotype ; Phenylthiourea ; Polymorphism, Single Nucleotide

Though initial report from Japan showed positive association of schizophrenia with dinucleotide repeat polymorphism in the NT-3 gene, subsequent studies showed mixed results. Therefore we conducted a replication study with Korean schizophrenics and matched controls who share similar ethnic background with Japanese population. The frequency of allele of dinucleotide repeat at 147 base pairs in the NT-3 gene was slightly increased, however, failed to reach statistical significance(X2=1.884, df=1, p<0.170) between the two groups. These findings do not support on association of NT-3 gene polymorphism with schizophrenia in Korean sample.
Alleles ; Asian Continental Ancestry Group ; Base Pairing ; Dinucleotide Repeats ; Humans ; Japan ; Schizophrenia

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

A Single Nucleotide Polymorphism (SNP) is a small genetic change or variation that can occur within a DNA sequence. It's the difference of one base at specific base pair position. SNP variation occurs when a single nucleotide, such as an A, replaces one of the other three nucleotide letters-C, G, or T. On average, SNP occur in the human population more than 1 percent of the time. They occur once in every 300 nucleotides on average, which means there are roughly 10 million SNPs in the human genome. Because SNPs occur frequently throughout the genome and tend to be relatively stable genetically, they serve as excellent biological markers. They can help scientists locate genes that are associated with disease such as heart disease, cancer, diabetes. They can also be used to track the inheritance of disease genes within families. SNPs may also be associated with absorbance and clearance of therapeutic agents. In the future, the most appropriate drug for an individual could be determined in advance of treatment by analyzing a patient's SNP profile. This pharmacogenetic strategy heralds an era in which the choice of drugs for a particular patient will be based on evidence rather than trial and error (so called" personalized medicine").
Base Pairing ; Base Sequence ; Biomarkers ; Genome ; Genome, Human ; Heart Diseases ; Humans ; Precision Medicine ; Nucleotides ; Polymorphism, Single Nucleotide ; Track and Field ; Wills

The gene encoding the 66 kilodalton (kDa) protein of Borrelia hermsii HS1 was cloned and sequenced. Chromosomal DNA was prepared from purified B. hermsii and used in construction of genomic library. The library was screened for positive clones by 314 bp DIG-labeled probe synthesized on the basis of the part of the sequence of B. hermsii. Positive clone was subcloned into p2ErO vector and was designated as pBH11. pBH11 were subcloned into pBluscript vector and were designated as pBH11-1 (500 bp), pBH11-2 (800 bp), pBH11-3 (600 bp) and pBH11-4 (800 bp). The plasmids were sequenced and determined the nucleotide sequence of p66. The open reading frame of the p66 consisted of 1803 base pairs coding for 600 amino acid protein. The basic information on the p66 gene of B. hermsii HS1 obtained from this study will be useful for further analysis and experiment of pathogenesis of the borrelia.
Base Pairing ; Base Sequence ; Borrelia* ; Clinical Coding ; Clone Cells* ; Cloning, Organism* ; DNA ; Genomic Library ; Open Reading Frames ; Plasmids

Prediction of RNA secondary structures including pseudoknots is a difficult topic in RNA field. Current predicting methods usually have relatively low accuracy and high complexity. Considering that the stacking of adjacent base pairs is a common feature of RNA secondary structure, here we present a method for predicting pseudoknots based on covariance with stacking and minimum free energy. A new score scheme, which combined stacked covariance with free energy, was used to assess the evaluation of base pair in our method. Based on this score scheme, we utilized an iterative procedure to compute the optimized RNA secondary structure with minimum score approximately. In each interaction, helix of high covariance and low free energy was selected until the sequences didn't form helix, so two crossing helixes which were selected from different iterations could form a pseudoknot. We test our method on data sets of ClustalW alignments and structural alignments downloaded from RNA databases. Experimental results show that our method can correctly predict the major portion of pseudoknots. Our method has both higher average sensitivity and specificity than the reference algorithms, and performs much better for structural alignments than for ClustalW alignments. Finally, we discuss the influence on the performance by the factor of covariance weight, and conclude that the best performance is achieved when lambda1 : lambda2 = 5 : 1.
Algorithms ; Base Pairing ; Base Sequence ; Computational Biology ; methods ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA ; chemistry ; genetics ; Sequence Analysis, RNA

McLeod syndrome is a rare X-linked multisystem disorder which forms the core of neuroacanthocytosis syndrome. Neurological symptoms characterized by chorea, seizure, cognitive impairment, and psychosis mostly develop around the 5-6th decades, accompanied by multisystem involvement comprising neuropathy, myopathy, acanthocytosis and hepatosplenomegaly. We hereby present a 60-year-old male who is the first genetically confirmed Korean McLeod syndrome patient. Genetic analysis of his XK gene revealed a previously reported 5 base pair deletion of exon 3 (c.856_860delCTCTA).
Abetalipoproteinemia ; Base Pairing ; Chorea ; Cognition Disorders ; Exons ; Humans ; Korea* ; Male ; Middle Aged ; Muscular Diseases ; Neuroacanthocytosis ; Psychotic Disorders ; Seizures

PURPOSE: MEN1 gene mutation causes multiple endocrine neoplasia type 1. It also suggests that somatic MEN1 gene mutation plays a role in sporadic endocrine tumor. In this study, we examined whether somatic mutations of MEN1 gene are responsible for sporadic parathyroid tumors and correlate with clinical manifestations of parathyroid tumors. METHODS: Somatic mutation of MEN1 gene in the formalin-fixed, paraffin-embedded parathyroid tumor tissue from 8 adenomas, 2 carcinomas and 1 hyperplasia were analyzed by direct sequencing. Clinicopathological parameters were reviewed from medical records and compared with the mutational data. RESULTS: Eight of eleven (73%) sporadic parathyroid tumors had somatic MEN1 mutations of 14 different types. In the 14 types, 13 were a point mutation which is composed of 8 missense mutations, 2 nonsense mutations and 3 silent mutations. One of 14 types is a frameshift deletion of 27 base pairs in exon 2. Somatic mutation was frequent in the exon 2 and exon 10. Four types of polymorphism were found. There was no correlation between the presence of mutations and clinicopathological phenotype of parathyroid tumors. CONCLUSION: This result suggests that somatic mutation of MEN1 gene plays a definite role in sporadic parathyroid tumor formation.
Adenoma ; Base Pairing ; Codon, Nonsense ; Exons ; Hyperplasia ; Medical Records ; Multiple Endocrine Neoplasia Type 1 ; Mutation, Missense ; Phenotype ; Point Mutation