Interleukin-6 and E-selectin in acute coronary syndromes and stable angina pectoris. A comparative study.

OBJECTIVES: The purpose of the study was to compare the serum levels of interleukin-6 (IL-6), E-selectin, and trans-fatty acids (TFA) between those with stable and unstable angina pectoris. METHODS: From September 2008 to March 2009, a case-control study was performed at two university hospitals. We included 89 patients with acute coronary syndrome (ACS) including patients with myocardial infarction and those with unstable angina pectoris (case group) and 93 patients with stable angina pectoris (control group). The two groups were matched with respect to demographic characteristics and risk factors of cardiovascular diseases. Serum levels of IL-6 and E-selectin were measured using the enzyme linked immunosorbent assay, while TFA and lipoproteins were measured using gas chromatography and enzymatic methods, respectively. RESULTS: No significant differences between baseline characteristics of the two study groups were observed. Patients with stable angina had significantly higher serum levels of total cholesterol (187.0 ± 3.7 vs. 171.6 ± 4.2 mg/dl; p = 0.009), low density lipoproteins (104.8 ± 2.4 vs. 95.4 ± 2.7; p = 0.017), and TFA (1.41 ± 0.47 vs. 1.24 ± 0.69 mg/dl; p = 0.047) compared to those with ACS. Serum levels of IL-6 were found to be significantly higher in those with stable angina compared to those with ACS (102.4 ± 1.9 vs. 224.6 ± 3.6; p = 0.007). However, patients with ACS had higher levels of E-selectin (53.5 ± 25.7 vs. 49.2 ± 23.5 µg/dl; p = 0.52), but the difference did not reach statistical significance. CONCLUSION: In the current study, inflammation as measured by IL-6 and E-selectin was not found to play an important role in progression of ischemic heart disease from stable angina to unstable angina or myocardial infarction, which is contrary to previous studies.

Monitoring iodine following consumption of iodized salt in Tehrani inhabitants.

As the production, distribution and consumption of iodized salt has increased in recent years, this study was carried out to assess iodine status in Tehran in 1996. 1146 families comprising 5140 subjects in the twenty districts of Tehran city from all age groups were randomly selected. Thyroid size was examined by palpation and graded according to the WHO classification. In 163 families selected randomly, thyroid size was determined by ultrasonography and urinary iodine was measured by digestion method. Serum T4, T3 and TSH (IRMA) concentrations were also assayed by kits. Percentage of grades 1 & 2 goiter were 44 & 44% in females and 49 & 33% in males respectively. Median urinary iodine was 17.5 micrograms/dl. Mean serum T4, T3 and TSH were 8.41 +/- 1.4 micrograms/dl, 170 +/- 37 ng/dl and 1.4 +/- 0.8 mu/ml, respectively. In 118 children aged 6-10 years median urinary iodine was 17.5 micrograms/dl. Thyroid volume in children was 4.3 +/- 1.9 ml. No correlation was established between the thyroid volume and goiter grade. This study points to the adequacy of iodine intake in the majority of families residing in Tehran.

Alternative splicing for the alpha1 subunit of soluble guanylate cyclase.

Soluble guanylate cyclase (sGC), the receptor for nitric oxide, is a heterodimer consisting of alpha and beta subunits. We investigated the mRNA species for the alpha(1) subunit in human brain, heart, artery and immortalized B-lymphocytes. Three mRNA species were identified in these tissues. The major mRNA species contained the full expression sequence of the alpha(1) subunit. Two other types of mRNA were detected in which 5' sequences were deleted by splicing (506-590 and 412-590). Each of these deletions included the predicted translation start site, indicating that translation of these two alternatively spliced RNA species does not result in the production of full-length alpha(1) subunits. The relative amounts of the two mRNA species with deletions of the translation start site differed significantly between cell lines of immortalized B-lymphocytes from different individuals. sGC enzymic activity was significantly decreased in cellular extracts from cell lines with high proportions of mRNA species containing the deletion 506-590 when compared with extracts from cell lines that contained mostly mRNA without this deletion.

A general approach to single-nucleotide polymorphism discovery.

Single-nucleotide polymorphisms (SNPs) are the most abundant form of human genetic variation and a resource for mapping complex genetic traits. The large volume of data produced by high-throughput sequencing projects is a rich and largely untapped source of SNPs (refs 2, 3, 4, 5). We present here a unified approach to the discovery of variations in genetic sequence data of arbitrary DNA sources. We propose to use the rapidly emerging genomic sequence as a template on which to layer often unmapped, fragmentary sequence data and to use base quality values to discern true allelic variations from sequencing errors. By taking advantage of the genomic sequence we are able to use simpler yet more accurate methods for sequence organization: fragment clustering, paralogue identification and multiple alignment. We analyse these sequences with a novel, Bayesian inference engine, POLYBAYES, to calculate the probability that a given site is polymorphic. Rigorous treatment of base quality permits completely automated evaluation of the full length of all sequences, without limitations on alignment depth. We demonstrate this approach by accurate SNP predictions in human ESTs aligned to finished and working-draft quality genomic sequences, a data set representative of the typical challenges of sequence-based SNP discovery.

Donor splice mutation (665 + 1 G_T) in familial hypobetalipoproteinemia with no detectable apoB truncation.

We report a 49-member four-generation kindred in which 11 members express familial hypobetalipoproteinemia (FHBL). In other kindreds, various truncated apoB species cosegregate with the FHBL phenotype. In contrast, no truncated apoB proteins were found by immunoblotting of plasma samples in this kindred. Previous linkage analysis showed strong linkage of FHBL to apoB markers. Nucleotide sequence analysis demonstrated a 665 + 1 G_T transition in the splice donor site of intron 5. This probably alters the accuracy and efficiency of mRNA splicing leading to the extremely low apoB levels in plasma. In addition, we detected four novel polymorphisms in the apoB gene.

Peak height pattern in dichloro-rhodamine and energy transfer dye terminator sequencing.

Establishing the pattern in peak heights within local sequence contexts improves the accuracy of base calling and the identification of DNA sequence variations in dye-terminator cycle sequencing. We have systematically examined pairs of sequence-tagged sites (STSs) that vary at only a single nucleotide to determine how base changes influence the peak heights of neighboring bases in sequencing traces generated by two recently commercialized dye-terminator chemistries, the dichloro-rhodamine (dRhodamine) and the energy transfer (BigDye) terminators. For sequencing traces generated with the dRhodamine terminators, the peak height of a particular base in 28 of 64 possible 3-base windows (44%) can be predicted by knowing just one or two bases 5' to the base in question. For those generated with the BigDye terminators, the peak height of a particular base in 23 of 64 possible 3-base windows (36%) can be predicted by knowing the local sequence context. When the peak heights are binned slightly differently, 75% (48 out of 64 cases) of the base peaks generated by both dRhodamine and BigDye terminators fall in the middle half, confirming that the peak patterns of these two new dye terminator chemistries are much more even than those found in the original rhodamine dye terminator sequences.

The homozygous complete hydatidiform mole: a unique resource for genome studies.

The most frequent type of complete hydatidiform mole is a 46, XX homozygote formed by the fertilization of an empty ovum by a single haploid sperm that later duplicates its chromosomes to give a diploid tumor. The homozygous nature of these complete hydatidiform moles makes them unique resources for human genome studies. They can serve as homozygous controls in the development of single nucleotide polymorphism (SNP) markers and provide a way to obtain long-range haplotypes that are useful in population studies. The use of a homozygous control makes it possible to estimate the allele frequencies of the SNP markers in any population by sequencing pooled DNA samples. In this report, we present evidence of homozygosity of a complete hydatidiform mole using 20 diallelic markers distributed across the genome. Furthermore, its usefulness as a homozygous control in SNP development and as a resource for long-range haplotype determination is demonstrated using 11 newly discovered loci in the BRCA2 region on chromosome 13q12-q13.

AmpliTaq DNA polymerase, FS dye-terminator sequencing: analysis of peak height patterns.

Taq DNA polymerases in which the phenylalanine is substituted by a tyrosine at position 667 (Taq F667Y) are members of a new class of DNA polymerases that incorporate chain-terminating dideoxyribonucleoside triphosphates (ddNTPs) much more efficiently than the wild-type Taq DNA polymerase. Improved incorporation of ddNTPs into DNA during cycle sequencing using AmpliTaq DNA polymerase, FS (Taq-FS, a member of the Taq F667Y family), and dye-labeled primers results in nearly uniform peak heights in the sequencing trace. This is not the case when dye-labeled ddNTPs are used in Taq-FS cycle sequencing reactions. While the rate of dye-terminator incorporation is more efficient with Taq-FS, the peak pattern is still highly variable and different from that produced by the wild-type enzyme. We have systematically examined pairs of sequence-tagged sites that vary at only a single nucleotide to determine how base changes influence the peak heights of neighboring bases in sequencing traces generated by the Taq-FS dye-terminator chemistry. In 31 of 64 possible 3-base windows (48%), we find that the peak height of a particular base can be predicted by knowing just one or two bases 5' to the base in question. We have also compared and contrasted the peak patterns produced by the Taq-FS enzyme with those previously identified for the wild-type enzyme. Establishing the patterns in peak heights within local sequence contexts can improve the accuracy of base-calling and the identification of polymorphisms/mutations when using the Taq-FS dye-terminator cycle-sequencing chemistry.

Increasing the information content of STS-based genome maps: identifying polymorphisms in mapped STSs.

Physical maps of the human genome are being constructed by many groups using a mapping strategy that relies on the development of sequence-tagged sites (STSs). Thousands of physically mapped STSs, representing hundreds of kilobases (kb) of unique human DNA sequence, have been generated by these efforts. Since sequence variations are found every 1-2 kb in the genome, it is possible to extract additional information from mapped STSs by scanning them for variations. By screening 154 of the STSs published by the Whitehead Institute/MIT Genome Center, we have identified 47 new DNA sequence polymorphisms among the 37.2 kb of unique DNA sequence contained in these STSs. Using a sequence-based approach to estimate allele frequencies for these variations, 29 of the substitution polymorphisms (1 in 1.3 kb) were found to have heterozygosities exceeding 32%. Our study shows that the information content of STS-based genome maps can be increased with minimal additional effort by scanning for DNA polymorphisms, and that ambiguities and errors in the initial STS sequence can be resolved and corrected in the process.

Peak height variations in automated sequencing of PCR products using Taq dye-terminator chemistry.

Direct sequencing of PCR products using Taq DNA polymerase with dye-labeled dideoxy chain terminators results in traces with uneven peaks. The peak height variations reflect the disproportionate rate of incorporation of deoxynucleotides vs. their analogs, a phenomenon that is highly dependent on the neighboring DNA sequence. Such peak height variations make it difficult to call bases correctly or to interpret whether or not a polymorphism is present. We have systematically examined pairs of sequence-tagged sites that vary at only one nucleotide to determine how a single base change will affect the peak heights of neighboring bases. We have found that the peak height of a particular base can often be predicted from the knowledge of just one or two nucleotides 5'- to the base in question. We have also observed several artifacts that occur consistently in the sequencing traces. These artifacts can be misinterpreted as polymorphisms or can obscure the real peak at that site. The empirically derived trends presented in this report can be utilized profitably when one is editing sequence data or examining them for polymorphisms and mutations.