Acute type-A aortic dissection with patent false lumen through to the abdominal aorta: effects of a conventional elephant trunk on malperfusion syndromes and narrowed true lumen.

BACKGROUND: Narrowed true lumen and patent false lumen through to the terminal aorta is a high-risk condition for malperfusion syndromes (MS) in acute type-A aortic dissection. It is important to ascertain how the true and false lumens behave after surgery. PATIENTS AND METHODS: We retrospectively investigated 45 patients with this pathology. The true lumen sizes at the narrowest levels above and below the superior mesenteric artery were followed by computed tomography after surgery (0-36 months). RESULTS: Thirty-seven MS were seen in 23 patients. Hospital mortality was 8.9%. The narrowed true lumen was not enlarged in the first 6 months with a patent false lumen. The elephant trunk procedure did not improve the true lumen size. An extremely narrowed (≤3 mm) true lumen was associated with a significantly high incidence of MS and mortality. CONCLUSIONS: High incidences of MS were observed in this particular pathology. An extremely narrowed true lumen was accompanied by a high incidence of MS and mortality.

Computational Fluid Dynamics Using a Porous Media Setting Predicts Outcome after Flow-Diverter Treatment.

BACKGROUND AND PURPOSE: Knowledge about predictors of the outcome of flow-diverter treatment is limited. The aim of this study was to predict the angiographic occlusion status after flow-diverter treatment with computational fluid dynamics using porous media modeling for decision-making in the treatment of large wide-neck aneurysms. MATERIALS AND METHODS: A total of 27 patients treated with flow-diverter stents were retrospectively analyzed through computational fluid dynamics using pretreatment patient-specific 3D rotational angiography. These patients were classified into no-filling and contrast-filling groups based on the O'Kelly-Marotta scale. The patient characteristics, morphologic variables, and hemodynamic parameters were evaluated for understanding the outcomes of the flow-diverter treatment. RESULTS: The patient characteristics and morphologic variables were similar between the 2 groups. Flow velocity, wall shear stress, shear rate, modified aneurysmal inflow rate coefficient, and residual flow volume were significantly lower in the no-filling group. A novel parameter, called the normalized residual flow volume, was developed and defined as the residual flow volume normalized by the dome volume. The receiver operating characteristic curve analyses demonstrated that the normalized residual flow volume with an average flow velocity of ≥8.0 cm/s in the aneurysmal dome was the most effective in predicting the flow-diverter treatment outcomes. CONCLUSIONS: It was established in this study that the hemodynamic parameters could predict the angiographic occlusion status after flow-diverter treatment.

Cytokeratins 18 and 8 are poor prognostic markers in patients with squamous cell carcinoma of the oesophagus.

BACKGROUND: Cytokeratins (CKs) are structural marker proteins specific for epithelial cells. However, recent studies indicate their involvement in cancer progression. METHODS: We evaluated CK18 and its filament partner, CK8 expression, by immunohistochemistry in 210 resected specimens from patients with oesophageal squamous cell carcinoma (OSCC). We also analysed the relationship between their expression and various clinicopathological parameters including prognosis. RESULTS: Neither CK18 nor CK8 was expressed in non-cancerous squamous epithelium whereas proper oesophageal glands expressed both CKs. Ninety (42.9%) tumours were CK18 positive and 85 (40.5%) CK8 positive, and the concordance rate for immunohistochemical classification for CK18 and CK8 was 82.4%. CK18 expression correlated with poorly differentiated tumours, use of neo-adjuvant chemotherapy, and advanced stage. Prognosis of patients with CK18-positive tumours was poorer than that of patients with negative OSCC (P<0.001). A similar trend was noted for CK8 expression. Multivariate analysis identified pT (P=0.020), pN number (P=0.001), and CK18 expression (P=0.004) as independent prognostic factors. CK18 expression in 83 pretreatment biopsy specimens was detected in 47 cases (56.6%) and also correlated with prognosis (P=0.045). CONCLUSION: CK18/CK8 expression correlated with progression of OSCC. The significant correlation with prognosis and stable expression in biopsy specimen suggest usefulness of CK18 in selection of treatment strategies for OSCC.

Solution structure of the activator contact domain of the RNA polymerase alpha subunit.

The structure of the carboxyl-terminal domain of the Escherichia coli RNA polymerase alpha subunit (alpha CTD), which is regarded as the contact site for transcription activator proteins and for the promoter UP element, was determined by nuclear magnetic resonance spectroscopy. Its compact structure of four helices and two long arms enclosing its hydrophobic core shows a folding topology distinct from those of other DNA-binding proteins. The UP element binding site was found on the surface comprising helix 1, the amino-terminal end of helix 4, and the preceding loop. Mutation experiments indicated that the contact sites for transcription activator proteins are also on the same surface.

Distance determination in human ubiquitin by pulsed double electron-electron resonance and double quantum coherence ESR methods.

Recently, distance measurements by pulsed ESR (electron spin resonance) have been obtained using pulsed DEER (double electron-electron resonance) and DQC (double quantum coherence) in SDSL (site directed spin labeling) proteins. These methods can observe long range dipole interactions (15-80A). We applied these methods to human ubiquitin proteins. The distance between the 20th and the 35th cysteine was estimated in doubly spin labeled human ubiquitin. Pulsed DEER requires two microwave sources. However, a phase cycle is not usually required in this method. On the other hand, DQC-ESR at X-band ( approximately 9GHz) can acquire a large echo signal by using pulses of short duration and high power, but this method has an ESEEM (electron spin echo envelope modulation) problem. We used a commercial pulsed ESR spectrometer and compared these two methods.

Fission yeast pap1-dependent transcription is negatively regulated by an essential nuclear protein, crm1.

The fission yeast pap1+ gene encodes an AP-1-like transcription factor that contains a leucine zipper motif. We identified a target gene of pap1, the p25 gene. The 5' upstream region of the p25 gene contains an AP-1 site, and by DNase I footprint analysis, we showed that the pap1 protein binds to the AP-1 site as well as to a 14-bp palindrome sequence. p25 is overproduced when the pap1+ gene is overexpressed, whereas p25 is not produced at all in the pap1 deletion mutant. p25 was previously found to be overproduced in strains carrying cold-sensitive crm1 mutations whose gene product is essential for viability and is thought to play an important role in maintenance of a proper chromosomal architecture. Deletion and site-directed mutagenesis of sequences upstream of the p25 gene demonstrated that the AP-1 site as well as the palindrome sequence are crucial for transcriptional activation either by pap1 overproduction or by the cold-sensitive crm1 mutation; pap1+ is apparently negatively regulated by crm1+. Moreover, we found that cold-sensitive crm1 mutations are suppressed by the deletion of pap1+, further indicating a close relationship between crm1+ and pap1+. The crm1 protein is highly conserved; the budding yeast homolog, CRM1, which complements the fission yeast cold-sensitive crm1 mutation, was isolated and found to also be essential for viability. These results suggest the functional importance of chromosome structure on the regulation of gene expression through the pap1 transcription factor.

Mechanism of transcriptional regulation by methyl-CpG binding protein MBD1.

MBD1 is a mammalian protein that binds symmetrically methylated CpG sequences and regulates gene expression in association with DNA methylation. This protein possesses a conserved sequence, named methyl-CpG binding domain (MBD), among a family of methyl-CpG binding proteins that mediate the biological consequences of the methylation. In addition, MBD1 has at least five isoforms due to alternative splicing events, resulting in the presence of CXXC1, CXXC2, and CXXC3 in MBD1 isoforms v1 (MBD1v1) and MBD1v2, and CXXC1 and CXXC2 in MBD1v3 and -v4. In the present study, we have investigated the significance of MBD, CXXC, and the C-terminal transcriptional repression domain (TRD) in MBD1. A bacterially expressed MBD binds efficiently to densely methylated rather than to sparsely methylated DNAs. In both methylation-deficient Drosophila melanogaster SL2 cells and mammalian CHO-K1 cells, MBD1v1 represses transcription preferentially from both unmethylated and sparsely methylated promoters, while MBD1v3 inhibits densely methylated but not unmethylated promoter activities. The CXXC3 sequence in MBD1v1 is responsible for the ability to bind unmethylated promoter. Furthermore, we have constructed mutant-type MBD1s in which the functionally important residues Arg22, Arg30, Asp32, Tyr34, Arg44, Ser45, and Tyr52 are changed to alanine to investigate the correlation between the structure and function of the MBD in MBD1. Excepting those for Ser45 and Tyr52, none of the recombinant MBD mutants bound to the densely methylated or unmethylated DNAs, and green fluorescent protein-fused MBD1 mutants did not localize properly in the nucleus. All the MBD1v1 and -v3 mutants lost the activity of methylation-dependent gene repression. Based on these findings we have concluded that MBD1 acts as a transcriptional regulator depending on the density of methyl-CpG pairs through the cooperation of MBD, CXXC, and TRD sequences.

Solution structure of the IRF-2 DNA-binding domain: a novel subgroup of the winged helix-turn-helix family.

BACKGROUND: The transcription of interferon (IFN) and IFN-inducible genes is mainly regulated by the interferon regulatory factor (IRF) family of proteins, which recognize a unique AAGTGA hexamer repeat motif in the regulatory region of IFN genes. A DNA-binding domain of approximately 100 amino acids has been commonly found in the IRF family of proteins, but it has no sequence homology to known DNA-binding motifs. Elucidation of the structures of members of the IRF family is therefore useful to the understanding of the regulation and evolution of the immune system at the structural level. RESULTS: The solution structure of the DNA-binding domain of interferon regulatory factor-2 (IRF-2) has been determined by NMR spectroscopy. It is composed of a four-stranded antiparallel beta sheet and three alpha helices, and its global fold is similar to those of the winged helix-turn-helix (wHTH) family of proteins. A long loop (Pro37-Asp51) is found immediately before the HTH motif, which is not found in other wHTH proteins. The NMR signals of residues in this long loop, as well as the second helix of the HTH motif, are strongly affected upon the addition of the hexamer repeat DNA, suggesting that these structural elements participate in DNA recognition and binding. CONCLUSIONS: The structural similarity of the DNA-binding domain of IRF-2 with those of proteins in the wHTH family shows that the IRF proteins belong to the wHTH family, even though there is no apparent sequence homology among proteins of the two families. The sequential structure alignment program (SSAP) shows that IRF-2 has a slightly different structure from typical wHTH proteins, mainly in the orientation of helix 2. The IRF family of proteins should therefore be categorized into a subfamily of the wHTH family. The evidence here implies that the evolutional pathway of the IRF family is distinct from that of the other wHTH proteins, in other words, the immune system diverged from an evolutional stem at an early stage.

Inhibition of soybean lipoxygenase-1 by n-alcohols and n-alkylthiols.

A series of n-alcohols and n-alkylthiols with carbon chains from 2 to 12 were examined for the inhibition of soybean lipoxygenase-1 (L-1). The alcohol produces a competitive inhibition, the extent of which increases with an increase in the carbon number of alkyl chain up to 8. Whereas the inhibition of the alkylthiol is noncompetitive, the extent of which is almost independent from the carbon number. From the behavior of pKi dependence on the carbon number of the alcohol, the decyl group appears to be optimum to bind to L-1. The thermodynamic analysis for the inhibition based upon van 't Hoff equation indicates positive enthalpy and entropy changes for the binding of the alcohol to the enzyme and negative enthalpy and positive to negative entropy changes for that of the alkylthiol. These observations suggest that the alcohol inhibits L-1 by binding of the hydrophobic alkyl tail to the catalytic site of the enzyme by a hydrophobic interaction. The alkylthiol inhibits by binding of the nucleophilic sulfhydryl head to a polarizable region of the enzyme and the alkyl tail to a hydrophobic region of the enzyme free from the steric hindrance as an anchor.

Lysophosphatidylcholine from white muscle of bonito Euthynnus pelamis (Linnaeus): involvement of phospholipase A1 activity for its production.

A fairly large amount of lysophosphatidylcholine (LPC) was detected in the fresh muscle of bonito Euthynnus pelamis (Linnaeus). The major fatty acid esterified in LPC were highly unsaturated fatty acids, such as docosahexaenoic and eicosapentaenoic acids, and the form was mainly composed of 1-lyso-2-acyl-sn-glycero-3-phosphocholine (1-LPC). The content of this species continued to increase during 4 months of frozen storage and then decreased. Phospholipase A1 activity detected in the bonito muscle was supposed to be responsible for the accumulation of LPC.

Site-specific cleavage of tRNA by imidazole and/or primary amine groups bound at the 5'-end of oligodeoxyribonucleotides.

Sequence specific RNA cleaving molecules were synthesized by attaching novel polyamine derivatives bearing imidazole and/or primary amine groups to the 5'-end of DNA oligonucleotides as the sequence-recognizing moieties. The actions of the molecules on a half-tRNA(Asp) were investigated. The oligonucleotides directed the nuclease activity (the imidazole and the primary amine are the catalytic groups) of the enzyme to the nucleotides directly adjacent to the complementary target sequence on the substrate RNA. The cleavage reaction shows a bell-shaped pH dependence with a maximum at pH 7.0, indicating the participation of protonated and non-protonated imidazoles residues in the process. The specificity of these hybrid enzymes can be easily altered, and they should prove to be useful tools for probing RNA structures in solution and as potential reactive groups in antisense oligonucleotide derivatives. We also describe the site-specific cleavage of tRNA(Asp) by the cleaving reagents bearing imidazole and/or primary amine groups at the 5'-end of oligodeoxyribonucleotides.

Three-dimensional dimer structure of the lambda-Cro repressor in solution as determined by heteronuclear multidimensional NMR.

The 1H, 15N and 13C magnetic resonances of the lambda-Cro repressor have been assigned almost completely, mainly through the use of heteronuclear multidimensional NMR methods. Inter-subunit NOEs were distinguished by means of heteronuclear spectral editing technique (13C double half filter technique). Based on the distance and dihedral angle constraints derived from the NMR data, the three-dimensional solution structure of the lambda-Cro repressor in the dimeric form has been calculated by the simulated annealing method. The input for the structure calculations consisted of 1H-1H distance constraints, of which 1536 were intra-subunit and 40 were inter-subunit, and dihedral angle, phi, constraints, which numbered 92. The average root-mean-square deviation (RMSD) for all backbone heavy- atoms of the 20 calculated structures for residues 3 to 59 of the total of 66 amino acid residues in both subunits was 1.57 Angstrum, while the average RMSD for each subunit in the same residue range was 0.66 Angstrum. The subunit is composed of three alpha-helices, residues 7 to 13, 16 to 23 and 27 to 36, and a three-stranded anti-parallel beta-sheet composed of residues 3 to 6, 40 to 44 and 50 to 55. The solution structure of the subunit is essentially the same as that in the crystalline form, but the structure of the dimer form in solution differs from that of the dimer unit in the crystalline form. It is suggested that the solution dimer structure is distorted to fit the recognition helices in the major grooves of DNA on complex formation.

Crystallographic characterization of a PHO4-DNA complex.

Crystals have been obtained of the DNA-binding domain of the yeast transcription factor PHO4 in complexes with several synthetic fragments of DNA with appropriate cognate sequences. Crystals suitable for X-ray diffraction studies were produced in the case of a complex of the protein with a 17 base-pair fragment of DNA from a solution in polyethylene glycol and calcium chloride. The crystals have the space group of P4(1)2(1)2 or P4(3)2(1)2 with unit cell dimensions a = b = 56.7 A, c = 447.8 A. The diffraction data at 3 A resolution were collected using synchrotron radiation with a Weissenberg camera for macromolecular crystallography.

[Advantages of side-to-side anastomosis in the assessment and revision of coronary artery bypass grafting].

With the advent of drug eluting stents in percutaneous coronary intervention, required quality level of coronary artery bypass grafting (CABG) has been elevating. To obtain nearly perfect patency of bypass grafts, intraoperative assessment and repair of abnormal grafts are helpful. We report systematic revision and safe repair technique of arterial grafts in CABG. Side-to-side instead of commonly used end-to-side anastomosis of arterial grafts is the first step in this technique. When any abnormalities are noted in intraoperative flowmetry of a graft, the distal surgical clip is removed. Free flow of the graft is measured. A coronary probe is gently inserted into the graft and the coronary artery. Vasodilators can be injected into the graft if necessary. When direct revision of the anastomosis is indicated, the graft is cut longitudinally from the distal end up to just proximal to the anastomotic site. The shape of the anastomosis can be observed directly without removing sutures. When re-anastomosis is not indicated, the distal remnant graft tissue is folded back and utilized as a patch. Thus the graft can be easily closed without narrowing.

[The correlation between flow pattern during cardiopulmonary bypass and patency of the coronary artery bypass grafts].

Recently the availability of transit time flow measurement (TTFM) is reported especially in off-pump coronary artery bypass grafting (CABG). But little is known about TTFM findings in on-pump CABG. We examined the correlation between the TTFM flow pattern and the angiography findings in on-pump CABG. The subjects consisted of 52 patients who underwent on-pump CABG and angiography early after operation. In these patients, 55 internal thoracic artery (ITA), 17 gastroepiploic artery (GEA), 13 saphenous vein graft (SVG) and 41 radial artery (RA) were tested with TTFM during cardiopulmonary bypass (CPB). TTFM demonstrated a diastolic filling pattern in 53 ITA, 16 GEA, 13 SVG and 36 RA. The angiography revealed that all these grafts were perfectly patent with the exception of a GEA with a flow competition pattern. TTFM revealed an abnormal flow pattern in 2 ITA (these 2 grafts were revised during CPB and the angiography demonstrated their perfect patency), 1 GEA (to and fro pattern), 0 SVG and 5 RA (the abnormal pattern was due to graft spasm in 3 of 5, and the angiography revealed their perfect patency, however, the angiography detected stenosis in the remaining 2 grafts). The present study found that the TTFM flow pattern during CPB correlated well with the angiography findings. TTFM during CPB was useful to detect graft failure, and grafts were revised safely during CPB.

Morphologic Features of Carotid Plaque Rupture Assessed by Optical Coherence Tomography.

BACKGROUND AND PURPOSE: Rupture of the plaque fibrous cap and subsequent thrombosis are the major causes of stroke. This study evaluated morphologic features of plaque rupture in the carotid artery by using optical coherence tomography in vivo. MATERIALS AND METHODS: Thirty-six carotid plaques with high-grade stenosis were prospectively imaged by optical coherence tomography. "Plaque rupture" was defined as a plaque containing a cavity that had overlying residual fibrous caps. The fibrous cap thickness was measured at its thinnest part for both ruptured and nonruptured plaques. The distance between the minimum fibrous cap thickness site and the bifurcation point was also measured. Optical coherence tomography identified 24 ruptured and 12 nonruptured plaques. RESULTS: Multiple ruptures were observed in 9 (38%) patients: Six patients had 2 ruptures in the same plaque, 2 patients had 3 ruptures in the same plaque, and 1 patient had 5 ruptures in the same plaque. Most (84%) of the fibrous cap disruptions were identified at the plaque shoulder and near the bifurcation point (within a 4.2-mm distance). The median thinnest cap thickness was 80 µm (interquartile range, 70-100 µm), and 95% of ruptured plaques had fibrous caps of <130 µm. Receiver operating characteristic analysis revealed that a fibrous cap thickness of <130 µm was the critical threshold value for plaque rupture in the carotid artery. CONCLUSIONS: Plaque rupture was common in high-grade stenosis and was located at the shoulder of the carotid plaque close to the bifurcation. A cap thickness of <130 µm was the threshold for plaque rupture in the carotid artery.

Structure of the Oct-3 POU-homeodomain in solution, as determined by triple resonance heteronuclear multidimensional NMR spectroscopy.

The POU-homeodomain (POUH) forms the bipartite DNA-binding POU domain in association with the POU-specific domain. The 1H, 15N, and 13C magnetic resonances of the 67-amino acid long POUH of mouse Oct-3 have almost completely been assigned, mainly through the combined use of three-dimensional triple resonance NMR methods. Based on the distance and dihedral angle constraints derived from the NMR data, the solution structure of the POUH domain has been calculated by the ab initio simulated annealing method. The average RMS deviation for all backbone heavy atoms of the 20 best calculated structures for residues 9-53 of the total 67 amino acid residues is 0.44 A. The POUH domain consists of three alpha-helices (helix-I, 10-20; helix-II, 28-38; and helix-III, 42-53), and helices-II and -III form a helix-turn-helix motif. In comparison with other classical homeodomains, the folding of the three helices is quite similar. However, the length of helix-III is fairly short. In the complex of the Oct-1 POU domain with an octamer site (Klemm JD, et al., 1994, Cell 77:21-32), the corresponding region is involved in helix-III. The structural difference between these two cases will be discussed.

Plasmid vectors designed for high-efficiency expression controlled by the portable recA promoter-operator of Escherichia coli.

A novel expression vector using the 236-bp promoter-operator fragment of the recA gene (recApo) of Escherichia coli has been constructed. This DNA fragment contains complete signals for the initiation of RNA synthesis, as well as for regulation by the lexA product, but lacks the coding sequence for the RecA protein. The strength of the recA promoter was examined by assaying beta-galactosidase activity expressed from a cro-lacZ fused gene placed downstream of the promoter. Under noninducing conditions, the promoter was regulated by the LexA protein, and the fused gene was expressed only weakly. Upon induction by nalidixic acid in a recA+ strain, high expression was observed for an extended period. After 5 h under inducing conditions, as much as 11% of the total cellular protein was cro-lacZ product. The expression level was higher than that from promoters of lac, trp, and lambda early genes.

Determination of the DNA binding site of the GAL4 protein. A photo-CIDNP study.

After the assignment of 1H NMR signals of aromatic side chains by means of specific deuteration, we analyzed the DNA binding site of GAL4 by measuring photo-CIDNP spectra. The results showed that Trp36 is involved in both the specific interaction with UASG and non-specific DNA binding. This residue is located inside the Cys-rich region, but outside the putative Zn-finger. The photo-CIDNP spectrum also showed that the side chains of Tyr40 and His53 are not exposed on the surface of the protein.

Secondary structure and folding topology of the DNA binding domain of interferon regulatory factor 2, as revealed by NMR spectroscopy.

The secondary structure elements of the DNA-binding domain of mouse interferon regulatory factor 2 [IRF-2(113)] were determined by heteronuclear multidimensional NMR spectroscopy. The sequential NOE connectivities, amide proton exchange rates, and 3JHN alpha coupling constants indicated the presence of three alpha-helical regions and four short beta-strands connected through relatively long loops. The long range NOEs indicated the four strands form an antiparallel beta-sheet and the three alpha-helices form a bundle on the sheet. The arrangement of the secondary structure elements and the overall folding topology resemble those of the DNA binding domains of bacterial activator CAP, heat shock transcription factors, and fork-head proteins, although there is no sequence homology among them.