The appearance of cartilage used in deep inferior epigastric perforator breast reconstruction surgery as a calcified mass on CT scan.

This paper describes an unusual radiological appearance of implanted cartilage on CT scan in a patient who had recently undergone deep inferior epigastric perforator (DIEP) breast reconstruction surgery following a mastectomy for ductal carcinoma in situ. The purpose of this paper is to alert medical practitioners involved with DIEP breast reconstruction surgery, as well as general radiologists, to the possibility of surgically implanted costal cartilage undergoing calcification and then appearing on imaging studies as a malignant process. Information on the patient was gathered from clinical records, imaging reports and pathological samples. A literature search was performed to identify similar cases and the results showed that this occurrence has never before been described and therefore represents an advancement of knowledge about the imaging characteristics of reconstructed breast tissue.

Tricross : using dot-plots in sequence-id space to detect uncataloged intergenic features.

MOTIVATION: The process of determining the functional sequence content of an organism is confounded by several factors. Large protein coding sequences are relatively easy to find by statistical methods. Smaller proteins however may escape detection due to their size falling below some arbitrary researcher-defined minimum cutoff, or the inability to precisely define a promoter, or translational start (Delcher et al., Nucleic Acids Res., 27, 4636-4641, 1999). Promoter and regulatory sequences themselves are difficult to define due to a significant amount of allowable sequence variation, as well as a probable lack of any completely accurate whole-organismal gene catalogs to date. Finally, certain genes coding functional RNAs may have insufficient structural or sequence constraints to be detectable by normal sequence structure/pattern searching methods (Eddy and Rivas, Bioinformatics, 16, 583-605, 2000). In those cases where there are multiple closely related organisms that have been sequenced, there is additional information that may be used in the investigation of sequence content-that being the possible conserved nature of functional sequences between the organisms. We present a method for the utilization of this conserved information to detect genes and other potentially functional sequences that may be missed by standard ORF-calling, RNA finding, and pattern matching software. The tricross programs produce a multi-way cross comparison of three sets of sequences, determine which are conserved in all three sets, and produce a graphical (Virtual Reality Modelling Language-VRML; (ISO/IEC 14772-1: 1997, VDC), 1997) representation as well as alignments of all sequence triples found. The software can also be applied to a pair of sequence sets, though the noise in the results increases. RESULTS: Tricross has been used to examine the intergenic-sequence content of the three archaeal Pyrococcus genomes to determine the most highly related sequences remaining between the annotated protein and RNA coding sequences. Set to relatively stringent similarity requirements for the search, tricross found 101 intergenic sequences conserved among the three organisms. Interestingly, 29 of these appear to contain members of a family of small RNA molecules (Kiss-Laszlo et al., EMBO J., 17, 797-807, 1998) only recently discovered in the Archaea (Armbruster, OSU, Diss., 1988; Omer et al., Science, 288, 517-522, 2000; Gaspin et al., J. Mol. Biol., 297, 895-906, 2000). While some of the remaining 72 appear to be individual highly conserved promoter sequences, others have no currently known biological significance. Although originally developed to facilitate the examination of intergenic sequences, none of the tricross logic is inherently specific to intergenic sequences. The software can also be applied to gene sequences, and has been used to produce inter-genomic gene order dot-plots for Haemophilus influenzae (Fleischmann et al., Science, 269, 496-512, 1995) versus H.ducreyi (unpublished data), and Neisseria meningiditis Z2491 (serogroup A) (Parkhill et al., Nature, 404, 502-506, 2000) versus Neisseria meningiditis Z58 (serogroup B) (Tettelin et al., Science, 287, 1809-1815, 2000) versus Neisseria gonorrhoeae (Lewis et al., http://micro-gen.ouhsc.edu/, 2000). AVAILABILITY: The tricross software package is available from http://www.biosci.ohio-state.edu/~ray/bioinformatics/tricross.html. CONTACT: ray@biosci.ohio-state.edu; daniels.7@osu.edu; munsonr@pediatrics.ohio-state.edu SUPPLEMENTARY INFORMATION: Additional data from the cross-genomic comparisons examined in the discussion section are linked from http://www.biosci.ohio-state.edu/~ray/bioinformatics/tricross.html.

Evaluation of syncope in adult congenital heart disease.

Approximately one million adults in the United States have congenital heart disease. The practitioner who sees one of these patients presenting with syncope must have a thorough understanding of: the underlying disease process; the associated congenital heart abnormalities; the type of surgery performed; the potential surgical residua; and the natural and unnatural history of this type of heart disease. Several types of congenital heart disease including: atrial septal defects; ventricular septal defects; left-sided obstructive lesions; Ebstein Anomaly; tetralogy of Fallot; and transposition of the great arteries are reviewed.

Valvular hemodynamics and arrhythmias with exercise following the Ross procedure.

Pulmonary autograft aortic valve replacement (Ross procedure) is increasing in popularity, particularly in children and young adults. We performed a controlled study of pediatric and adult Ross procedure patients to evaluate postoperative exercise valvular hemodynamics and cardiac rhythm. Thirty-one patients and 24 controls underwent stress echocardiography. Doppler and 2-dimensional echocardiography assessed valvular hemodynamics and right and left ventricular size at baseline and after exercise. Electrocardiography monitored cardiac rhythm. Patients and controls had neoaortic and neopulmonic valve insufficiency ranging from none to moderate that improved or did not change with exercise. Baseline and exercise mean peak transaortic gradients were not significantly different between patients (baseline 6.3 +/- 3.8 mm Hg, exercise 12.8 +/- 7.3 mm Hg) and controls (baseline 6.7 +/- 2.5 mm Hg, exercise 14.3 +/- 5.2 mm Hg). However, baseline and exercise mean peak transpulmonic gradients were significantly different between patients (baseline 20.7 +/- 9.6 mm Hg, exercise 45.2 +/- 23.5 mm Hg) and controls (baseline 3.7 +/- 1.3 mm Hg, exercise 10.6 +/- 3.7 mm Hg). Significant exercise-induced arrhythmias occurred in 8 patients (26%) and no controls. Occurrence of arrhythmias correlated with an older age at surgery and age at study. After the Ross procedure, patients have valve competence and transaortic gradients similar to controls at baseline and with exercise. However, patients have significantly increased baseline and exercise transpulmonic gradients compared with controls. Furthermore, exercise-induced arrhythmias occurred frequently in our patient group and were associated with an older age at surgery and age at study.

The PACRAT system: an extensible WWW-based system for correlated sequence retrieval, storage and analysis.

With PACRAT (Patterns, Analyses, Correlations. Remote Archive Testbed) we present an online database solution to the problem of accessing high-confidence sequences with specific relationships to classes of genes, such as upstream intergenic regions attached to tRNA genes. In addition the software contains a data warehousing and analysis-facilitating suite to streamline the process of analyzing the collected data. An unexpected additional benefit of the system is that it also provides easy access to sequences of lower confidence, and may be of assistance in such things as resolving ORF-call conflicts in genomic annotation projects.

Genome sequence of Halobacterium species NRC-1.

We report the complete sequence of an extreme halophile, Halobacterium sp. NRC-1, harboring a dynamic 2,571,010-bp genome containing 91 insertion sequences representing 12 families and organized into a large chromosome and 2 related minichromosomes. The Halobacterium NRC-1 genome codes for 2,630 predicted proteins, 36% of which are unrelated to any previously reported. Analysis of the genome sequence shows the presence of pathways for uptake and utilization of amino acids, active sodium-proton antiporter and potassium uptake systems, sophisticated photosensory and signal transduction pathways, and DNA replication, transcription, and translation systems resembling more complex eukaryotic organisms. Whole proteome comparisons show the definite archaeal nature of this halophile with additional similarities to the Gram-positive Bacillus subtilis and other bacteria. The ease of culturing Halobacterium and the availability of methods for its genetic manipulation in the laboratory, including construction of gene knockouts and replacements, indicate this halophile can serve as an excellent model system among the archaea.

Expression and heat-responsive regulation of a TFIIB homologue from the archaeon Haloferax volcanii.

Multiple divergent genes encoding the eukaryal-like TFIIB (TFB) transcription initiation factor have been identified in the archaeon Haloferax volcanii. Expression of one of these TFB-encoding genes, referred to here as tfb2, was induced specifically in response to heat shock at the transcription level. A time course for tfb2 induction demonstrated that mRNA levels increased as much as eightfold after 15 min at 60 degrees C. A transcription fusion of the tfb2 promoter region with a stable RNA reporter gene confirmed the heat responsiveness of the tfb2 core promoter, and immunoblot analysis using antibodies generated against a recombinant His-tagged TFB2 showed that the protein levels of one TFB increased slightly in response to elevated temperatures. An archaeal consensus TATA element (5'-TTTATA-3') was located 110 bp upstream of the translation start site and appeared to be used for both basal and heat shock-induced expression. The long DNA leader region (79 bp) preceding the predicted AUG translation start codon for TFB2 contained a T-rich sequence element located 22 bp downstream of the transcription start site. Using an in vivo transcription termination assay, we demonstrated that this T-rich element can function as a sequence-dependent transcription terminator, which may serve to downregulate expression of the tfb2 gene under both non-heat shock and heat shock conditions.

Pharmacologic stress echocardiography. Dobutamine and arbutamine stress testing.

Pharmacologic stress testing is an important noninvasive method for evaluating patients with known or suspected coronary artery disease who are unable to adequately exercise. Pharmacologic stress echocardiography using dobutamine has been developed over the last 10 to 15 years as an alternative to vasodilator stress testing using nuclear perfusion imaging. As experience has grown, digital subtraction echocardiogram has been shown to be a safe, convenient, and reliable method for stress testing in a variety of patient populations. Digital subtraction echocardiogram has comparable sensitivity, specificity, and accuracy when compared to other stress testing methods which employ cardiac imaging and is superior to the exercise echocardiogram. It has certain advantages over nuclear perfusion imaging in terms of cost and convenience. The recent addition of arbutamine echocardiography (which has been shown to be comparable to digital subtraction echocardiogram) provides another alternative method for pharmacologic stress testing. Continued improvement in echocardiographic image quality and the development of new technologies such as tissue harmonic imaging and contrast echocardiography will hopefully improve the echocardiographic evaluation of wall motion therefore increasing the diagnostic accuracy of echocardiographic stress testing.

Pulmonary homograft repair of a mycotic aortic aneurysm in an infant.

Thoracic aortic aneurysms are rare in children and even more unusual in infants. The vast majority are mycotic. Frequently, those with mycotic thoracic aortic aneurysm do not survive and the diagnosis is made at autopsy. We present the case of an asymptomatic infant found to have a mycotic thoracic aortic aneurysm. The clinical course, diagnosis, and surgical repair of the aneurysm with pulmonary homograft are discussed.

Heat shock inducibility of an archaeal TATA-like promoter is controlled by adjacent sequence elements.

The expression of a heat-inducible cct1 (chaperonin-containing Tcp-1) family member gene is regulated at the transcription level in the archaeon Haloferax volcanii. Transcriptional fusions of the cct1 promoter region with a yeast proline tRNA reporter gene were constructed to analyse the functional domains of this archaeal heat shock promoter. Both basal and heat-induced transcription of the reporter gene was directed by an archaeal consensus TATA element (5'-TTTATA-3') centred 25bp upstream of the transcription start site. Deletion mutagenesis indicated that the 5' boundary of the cct1 regulatory region mapped to position -37. Nucleotide alignment with the 5' flanking regions of two additional cct-related genes identified in H. volcanii showed a high degree of sequence conservation between positions +1 and -37, especially in and immediately surrounding the TATA element of the putative core promoter. Mutational analysis of conserved sequences demonstrated that basal and heat-induced transcription required sequence elements located upstream and downstream of the TATA-box. These findings indicate that the regulatory sequences involved in heat-induced transcription lie within the core promoter region and suggest that the mechanism controlling heat shock gene expression in H. volcanii differs from the bacterial and eukaryal strategies.

Reopening after successful coil occlusion for patent ductus arteriosus.

OBJECTIVES: This study was performed to determine the frequency of patent ductus arteriosus (PDA) reopening and the factors that may predict reopening after successful coil occlusion. BACKGROUND: Transcatheter coil occlusion is a widely used and accepted method to close a PDA. After documented successful coil occlusion, we found PDAs that reopened. We hypothesized that specific factors are involved in those that reopened. METHODS: All patients who underwent percutaneous transarterial PDA coil occlusion were studied. Successful coil occlusion was documented. PDA reopening was determined when Doppler-echocardiography (DE) performed after the procedure was negative for PDA flow but at follow-up demonstrated PDA shunting. Patients with a reopened PDA were compared with all other patients in evaluating independent variables. RESULTS: Coil occlusion for PDA was attempted in 22 patients. Clinical success was achieved in 20 patients (91%), and DE was negative for PDA shunting in 19 patients (90%). At follow-up, five patients demonstrated reopening. The PDA minimal diameter was 1.4 +/- 0.5 mm (mean +/- SD) for the reopened group and 1.2 +/- 0.7 mm for the other patients. The PDA length was 2.9 +/- 1.9 mm for the reopened group and 7.1 +/- 3.2 mm for all other patients. All those with type B PDA were in the reopened group. When independent variables were compared between groups, only PDA length and type B PDA predicted reopening (p < 0.05). CONCLUSIONS: PDA reopening may occur after successful coil occlusion. Short PDA length and type B PDA are associated with reopening. The data suggest that in such anatomy, alternative strategies to the current coil occlusion technique should be considered.

Common cardiac diseases in adolescents.

Adolescent patients frequently present with symptoms potentially referable to the cardiovascular system; however, patients rarely have true cardiovascular disease. In many patients, the history is the key to determining whether additional testing or referral is necessary. Even though the history, physical examination, and preliminary laboratory data may indicate a benign cause, occasionally a referral to a cardiologist is necessary because of patient or parental anxiety. Patients with true cardiac pathology should be followed by a cardiologist in conjunction with the primary care physician.

Acute pulmonary toxicity in an infant from intravenous amiodarone.

Intravenous amiodarone is an effective treatment for supraventricular and ventricular tachyarrhythmias. We report a case of acute pulmonary toxicity in an infant from intravenous amiodarone and describe the clinical evaluation and laboratory studies leading to the diagnosis.

Characterization of two heat shock genes from Haloferax volcanii: a model system for transcription regulation in the Archaea.

The expression of two heat-responsive cct (chaperonin-containing Tcp-1) genes from the archaeon Haloferax volcanii was investigated at the transcription level. The cct1 and cct2 genes, which encode proteins of 560 and 557 amino acids, respectively, were identified on cosmid clones of an H. volcanii genomic library and subsequently sequenced. The deduced amino acid sequences of these genes exhibited a high degree of similarity to other archaeal and eucaryal cct family members. Expression of the cct genes was characterized in detail for the purpose of developing a model for studying transcription regulation in the domain Archaea. Northern (RNA) analysis demonstrated that the cct mRNAs were maximally induced after heat shock from 37 to 55 degrees C and showed significant heat inducibility after 30 min at 60 degrees C. Transcription of cct mRNAs was also stimulated in response to dilute salt concentrations. Transcriptional analysis of cct promoter regions coupled to a yeast tRNA reporter gene demonstrated that 5' flanking sequences up to position -233 (cct1) and position -170 (cct2) were sufficient for promoting heat-induced transcription. Transcript analysis indicated that both basal transcription and stress-induced transcription of the H. volcanii cct genes were directed by a conserved archaeal consensus TATA motif (5'-TTTATA-3') centered at -25 relative to the mapped initiation site. Comparison of the cct promoter regions also revealed a striking degree of sequence conservation immediately 5' and 3' of the TATA element.

Splicing of intron-containing tRNATrp by the archaeon Haloferax volcanii occurs independent of mature tRNA structure.

We have investigated the requirements for mature tRNA structure in the in vivo splicing of the Haloferax volcanii, intron-containing tRNATrp RNA. A partial tRNATrp gene, which contained only the anticodon stem-loop region of the mature tRNA, was fused to a carrier yeast tRNA gene for expression in H. volcanii. Transcripts from this hybrid gene were found to be processed by endonuclease and ligase at the tRNATrp exon-intron boundaries. These results verify that the substrate recognition properties of the halobacterial endonuclease observed in vitro reflect the properties of this enzyme in vivo, namely that mature tRNA structure is not essential for recognition by the endonuclease. The independence of these reactions on mature tRNA provides further support for a relationship between archaeal tRNA and rRNA intron-processing systems and highlight a difference in the substrate recognition properties between the archaeal and eucaryal processing systems. The significance of these differences is discussed in light of the observation that the tRNA endonucleases of these organisms are related.

Properties of H. volcanii tRNA intron endonuclease reveal a relationship between the archaeal and eucaryal tRNA intron processing systems.

To better understand the relationship between archaeal and eucaryal tRNA introns and their processing systems, we have cloned the gene encoding the tRNA intron endonucleases from the archaeon H. volcanii. The gene encodes a 37 kDa protein that appears to be present as a homodimer under native conditions. Recombinant forms of this protein were expressed in E. coli and found to cleave precursor tRNAs lacking full mature tRNA structure, a property observed for the native endonuclease. Comparative sequence analysis revealed that similar proteins existed in other Archaea and that these proteins have significant similarity with two subunits of the yeast tRNA intron endonuclease. These results provide evidence that the archaeal and eucaryal tRNA intron processing systems are related and suggest a common origin for tRNA introns in these organisms.