Comprehensive study on iterative algorithms of multiple sequence alignment

Multiple sequence alignment is an important problem in the biosciences. To date, most multiple alignment systems have employed a tree-based algorithm, which combines the results of two-way dynamic programming in a tree-like order of sequence similarity. The alignment quality is not, however, high enough when the sequence similarity is low. Once an error occurs in the alignment process, that error can never be corrected. Recently, an effective new class of algorithms has been developed. These algorithms iteratively apply dynamic programming to partially aligned sequences to improve their alignment quality. The iteration corrects any errors that may have occurred in the alignment process. Such an iterative strategy requires heuristic search methods to solve practical alignment problems. Incorporating such methods yields various iterative algorithms. This paper reports our comprehensive comparison of iterative algorithms. We proved that performance improves remarkably when using a tree-based iterative method, which iteratively refines an alignment whenever two subalignments are merged in a tree-based way. We propose a tree-dependent, restricted partitioning technique to efficiently reduce the execution time of iterative algorithms.

[Complete resection of superior mediastinal seminoma, following reconstruction of superior vena cava--a case report]

The patient was a 37-year-old man with superior mediastinal seminoma, which invaded the bilateral brachiocephalic vein, superior vena cava, pericardium and left lung. These invaded organs were resected with the tumor and a vascular reconstruction was performed with EPTFE graft and pericardial patch. EPTFE graft was interposed between the left brachiocephalic vein and right atrium. Superior vena cava was reconstructed by means of pericardial patch. Histologically, the tumor was diagnosed as pure seminoma. He received the prophylactic irradiation (45 Gy). Although venography two years after operation demonstrated the obstruction of the EPTFE graft and marked stenosis of the pericardial patch, the patient remains free from the symptom and is doing well without recurrence 45 months after operation.

Screening of patients with ischemic heart disease by transesophageal atrial pacing and the selection of surgical therapy: in patients with arteriosclerosis obliterans and aortic aneurysm

This study evaluated (1) a screening method for ischemic heart disease (IHD) using transesophageal atrial pacing (TEP), and (2) the appropriate surgical therapy for patients with concomitant IHD which was evaluated on the basis of the coronary score (CS) by Leaman. Thirty-nine patients with arteriosclerosis obliterans of the lower extremities (ASO) and 35 with aortic aneurysm underwent TEP and coronary angiography (CAG). Coexistent IHD was diagnosed in 25 patients (64%) with ASO and in 14 (40%) with aortic aneurysm. Screening for IHD by TEP was 96% sensitive, 71% specific, and 87% accurate in patients with ASO, and 79% sensitive, 90% specific, and 86% accurate in patients with aortic aneurysm. Coronary artery bypass grafting (CABG) and peripheral arterial revascularization (PAR) were performed by one stage surgery in 3 patients with a CS of 16 or more. In 18 patients with a CS of 5.5 or less, only PAR was performed. One stage surgery was performed in 6 patients with aortic aneurysm. Four patients had a CS of 9.5 or more, and 2 patients with coexistent stenosis of the left anterior descending branch (LAD) had CS of 3.5 and 8, respectively. Repair of the aneurysm was undertaken in 5 patients with a CS of 8 or less without LAD disease. In patients with ASO showing a CS of 5.5 or less and in those with aortic aneurysm showing a CS of 8 or less (and without LAD disease), the only surgical procedure performed was either PAR or repair of the aneurysm. There were no complications attributable to IHD observed in these patients during the perioperative period.

Pharmacological properties of NK433, a new centrally acting muscle relaxant

The pharmacological properties of NK433 ((-)-(R)-2-methyl-3-(1-pyrrolidinyl)-4'-trifluoromethylpropiophenone+ ++ monohydrochloride), a novel muscle relaxant, were investigated. NK433 inhibited intercollicular decerebrate rigidity (gamma-rigidity) and anemic decerebrate rigidity (alpha-rigidity) dose dependently. NK433 was stronger in inhibiting gamma-rigidity than alpha-rigidity. NK433 inhibited the increase in muscle spindle discharges induced by pinna pinching (gamma-activity) without affecting muscle spindle discharges or neuromuscular transmission. At muscle relaxant doses in decerebrate rigidities, NK433 did not affect the muscle tone induced by morphine-HCl nor that of normal animals. These results suggest that NK433 selectively depresses the excessive muscle tone of decerebrate rigidities through its effects on the central nervous system, and inhibition of gamma-activity causes a preferential depression of gamma-rigidity in comparison to alpha-rigidity. In i.v. experiments, the effects of NK433 on decerebrate rigidities were similar to those of eperisone-HCl and tolperisone-HCl, but in p.o. experiments, NK433 was at least 3 times as potent as eperisone-HCl and tolperisone-HCl.

CRST syndrome (calcinosis cutis, Raynaud's phenomenon, sclerodactyly, and telangiectasia) associated with autoimmune hepatitis

A case of Raynaud's phenomenon, was complicated with autoimmune hepatitis (AIH) during the clinical course, and subsequently with gangrene of the fingertips caused by CRST syndrome (calcinosis cutis, Raynaud's phenomenon, sclerodactyly and telangiectasia). The presence of anticentromere antibodies is rare in AIH; to date, there has been only one report of a combination of AIH and CRST syndrome. This combination of the two diseases has been identified only in Japan.

Kinetic properties and structural characterization of highly purified acetyl-CoA synthetase from bovine heart and tissue distribution of the enzyme in rat tissues

Acetyl-CoA synthetase from bovine heart has been purified to homogeneity and been crystallized. The purification procedure involves ammonium sulfate precipitation and subsequent column chromatography on DEAE-Sepharose, Blue-Sepharose, CoA-Agarose and Superose 6. The purified enzyme has a specific activity of 45 units/mg protein, and its molecular weight estimated by sodium dodecyl sulfate polyacrylamide gel electrophoresis is approximately 72,000. The purified enzyme specifically utilizes acetate, ATP and CoA. Apparent Km values of the purified enzyme for acetate, CoA, and ATP were 0.16 mM, 0.14 mM and 0.25 mM, respectively. Limited digestion with trypsin, subtilisin BPN' and chymotrypsin revealed that the enzyme contains a 56 k segment resistant to these proteases. Secondary structure contents of the purified enzyme and the 56 k tryptic fragment were analyzed by circular dichroism measurement. The intact molecule contains 30% alpha-helix and 30% beta-structure, and trypsin digests alpha-helix rich regions more substantially. Western blot analysis of rat tissue homogenates by specific antibodies against the purified enzyme indicated that the 72 k enzyme is present in a wide variety of tissues and is most abundant in heart and kidney.

Hemodynamic changes in blood flow through the denervated liver in pigs

We investigated the effects of liver denervation on hemodynamic circulation in seven anesthetized pigs. Simultaneous measurements of the hepatic artery and portal vein were performed with an ultrasound Doppler flow meter before and after liver denervation. Neither resting systemic nor hepatic hemodynamics changed following liver denervation. However, temporary occlusion of the portal vein resulted in a significant increase in hepatic artery flow in the innervated liver (from 123 +/- 15 ml/min to 177 +/- 17 ml/min, p < .01), whereas, in the denervated liver, a significant decrease was observed (from 128 +/- 11 ml/min to 106 +/- 19 ml/min, p < .05). Thus, the reciprocity between the hepatic artery and portal vein in the hepatic artery flow during portal vein occlusion might intensify symptoms of portal vein thrombosis in liver transplantation. In the denervated liver, a significant decrease also occurred in systolic blood pressure and central venous pressure from 1 to 3 min after portal vein occlusion. Since the liver plays a crucial role in the maintenance of cardiovascular homeostasis during blood loss, it is likely that denervation at the porta hepatis induced a lack of vasoconstriction in the portal territory. Liver denervation might further exacerbate this response to hypotension. The current study confirms that the hepatic nerves play an important role in hepatic arterial and portal venous interactions aimed at maintaining a constant blood flow through the liver. We also suggest that the hepatic nerves are important for cardiovascular homeostasis.

Analysis of the p53 gene in human choriocarcinoma cell lines

In the present study, we analysed human choriocarcinoma cell lines for abnormalities in the tumour-suppressor gene p53 by Southern blotting, Northern blotting, non-radioisotopic single-stranded conformational polymorphism (SSCP) and complementary DNA sequencing. In all cell lines (Bewo, GCH-1, GCH-2, SCH, JAR, JEG-3, NUC-1 and HCCM-5), no p53 gene abnormality was detected by using Southern blotting. p53 mRNA of the expected size was detected in all cell lines tested by Northern blotting. SSCP analysis revealed abnormalities of p53 cDNA in the SCH cell line. Sequencing analysis of the entire coding region of the p53 gene revealed that both alleles were expressed in the JEG-3 cell line, and one of the alleles contained a point mutation (G to T) in codon 167 (Gln to His). In the NUC-1 cell line both alleles were point mutated. One allele had a point mutation (A to T) that resulted in a codon 17 change (Glu to Asp), and another had a point mutation (A to T) that caused a codon 24 change (Lys to Asn). In the SCH cell line, AGG was inserted between codon 249 and 250; this insertion resulted in an abnormal structure of the p53 protein. In three out of eight human choriocarcinoma cell lines, a p53 gene abnormality was detected. Therefore our data demonstrate that p53 gene abnormalities are associated with choriocarcinoma cell lines.

Suppressive effects of TNF-alpha on myelin formation in vitro

Using organotypic cultures of ICR mouse cerebellum, we studied the effects of TNF-alpha on myelin formation, and its demyelinating effects. Mature, myelinated cultures were resistant to TNF-alpha, even at the highest concentration examined, 1 x 10(4) U/ml. However, when cultures were grown in medium containing TNF-alpha from the time of explantation, myelin formation was significantly affected at a concentration of 1 x 10(2) U/ml. The myelin sheaths formed were very thin, partial, and few in number. When TNF-alpha was removed from the medium within 6 days, myelin formation was recovered. Although our in vitro system tests factors that influence myelin formation but not remyelination, these results suggest that TNF-alpha may be involved in the remyelination block following acute myelin breakdown.

Apoptosis in the degeneration process of unfertilized mouse ova

In mammals, ova which are not fertilized undergo degeneration. Thus, it seems that the ovum is programmed to die unless fertilization and embryogenesis occur, but little is known about the mechanism of such degeneration. To investigate this process, we observed the morphological changes of cultured unfertilized ova and stained DNA fragmentation by the modified TUNEL method (treating floating samples in liquid reagents) to detect apoptosis. Ova were collected from the oviducts of superovulated mice and cultured for observation. The number of morphologically abnormal ova with shrinkage of the ooplasm and cytoplasmic fragmentation, which are typical features of apoptosis, showed a significant gradual increase from 24 to 32 hr (p < 0.05) and an abrupt increase from 40 hr of incubation (p < 0.001). DNA fragmentation, which is one of the biological changes seen in apoptosis, was observed in the ooplasm of both intact and abnormal ova, cells with cytoplasmic fragmentation, and in the first polar body at the time of ovum collection as well as after incubation. These findings demonstrate that apoptosis is related to the process of degeneration in the mouse ovum and first polar body.

Influence of a cold front upon the onset of Meniére's disease in Toyama, Japan

In order to clarify the influence of a cold front (CF) upon the onset of Meniére's disease (MD), major CFs were defined by meteorological observations, and the influence of CFs on MD was evaluated by using the time n method. From our preliminary study it was seen that the onset of MD had its highest incidence exactly on days where a CF passed by. Out of the patients with MD, sudden deafness (SD) and Bell's palsy (BP) who visited our neurotological clinic of the Toyama Medical and Pharmaceutical University from 1987 to 1992, 67 MD patients, 70 SD patients and 70 BP patients could clearly define the date of the onset of their disease, and were therefore selected for this epidemiological study. Thirty-six our of the 67 MD patients had the first attack on the day when a CF passed by or on the next day. The results obtained from these studies were as follows. i) The onset of MD was influenced by the passing of a CF, and this influence was more specific in MD than in SD or BP. ii) In the 36 CF influence MD patients, the majority were over the forty years, and their hearing level was worse than that of the other 31 MD patients during the observation periods.

Evaluation of new medium with chromogenic substrates for members of the family Enterobacteriaceae in urine samples

A new medium containing 5-bromo-4-chloro-3-indolyl-beta-D-glucuronide cyclohexylammonium salt (Glu agar) for Escherichia coli and a new medium containing 5-bromo-3-indolyl-beta-D-galactoside (Gal agar) for beta-galactosidase-positive members of the family Enterobacteriaceae were compared with MacConkey agar in a diagnostic trial with 3,562 urine specimens. The isolation rates of E. coli and beta-galactosidase-positive Enterobacteriaceae were increased 8.4 and 19.5%, respectively. The sensitivities and specificities of Glu agar and Gal agar were 98.5 and 100% and 99.2 and 99.5%, respectively.

Alteration in circadian rhythm of plasma corticosterone in rats following sociopsychological stress induced by communication box

The purpose of present study was to investigate the physiological characteristics of sociopsychological stress induced by the communication box method. In this method, the nonfoot shocked rats were used as the psychological stressed experimental group. The stress exposure was loaded for 1 h between 0900 and 1000, daily. The changes in circadian rhythm of plasma corticosterone were studied following the 3-day, 5-day, or 10-day stress exposure, respectively. Plasma corticosterone levels of foot shocked rats and nonfoot shocked rats following the 3-day or 5-day stress exposure were significantly higher than those of control rats. Particularly, the marked elevation of plasma corticosterone was observed at the peak time of circadian rhythm (2100) in the both stress groups. Consequently, the amplitude of 24 h rhythm increased significantly, but the acrophase was not changed. However, the changes of plasma corticosterone levels of both stress groups following the 10-day stress exposure approached those of control group. These results suggest that the repeated exposure of sociopsychological stress can influence the circadian rhythm of plasma corticosterone. The communication box method may be a valuable tool for researching the etiology of human psychiatric disorders with rhythm disturbance.

[Basic and clinical studies on biapenem (L-627) in obstetrics and gynecology]

We investigated biapenem (BIPM, L-627) a newly carbapenem antibiotic, for its antibacterial activity, tissue penetration, clinical efficacy and bacteriological effect in obstetric and gynecological infections, and obtained the following results. 1. Antibacterial activity: MICs of L-627 against 149 strains isolated from 80 patients in this clinical trial were examined and compared with those of imipenem (IPM) and ceftazidime (CAZ). The MIC50 and MIC90 of L-627 against the isolates were 0.2 and 12.5 micrograms/ml, respectively. Those of IPM were 0.2 and 6.25 micrograms/ml, respectively. The antibacterial activity of L-627 was quite similar to that of IPM, and was superior to that of CAZ. 2. Tissue and retroperitoneal fluid penetration: The peak levels in venous and uterine arterial sera were 24.0 and 26.2 micrograms/ml, respectively, after 300 mg drip infusion. The peak levels in the uterine or adnexal tissues were 2.39-9.60 micrograms/g, and 0.2 microgram/g of L-627 was detected at 275 minutes after administration. Peak levels in retroperitoneal fluid were 8.7 +/- 1.7 micrograms/ml at 1 hour after the completion of 30 minutes drip infusion (300 mg) and 7.9 +/- 0.2 micrograms/ml at 30 minutes after 300 mg 60 minutes drip infusion (300 mg). These levels expected the MICs against main pathogenic organisms. 3.

CLINICAL RESULTS

L-627 was given to the following 144 patients (No. of analytical subjects) at a daily dose of 0.3-1.2 g for 2-13 days: intrauterine infections (54), adnexitis (36), parametritis (17), pelvic peritonitis (27), bartholins abscess (6) and other infections (4). The clinical efficacy was 93.1% (134/144) and the eradication rate against isolated organisms was 88.7% (110/124). Side effects were observed in 2 patients: eruption (1) and vomiting with numbness of the tongue (1). Abnormal change in laboratory test results included increase in eosinophils in 1, increase in GOT, GPT and gamma-GTP in 1 and increase in GPT and A1-P in 1, but all of these abnormalities were very mild and withdrawal of the drug was not required. Our results suggest that this drug is useful in the treatment of gynecological infections.

Attenuated endothelium-dependent peripheral vasodilation and clinical characteristics in patients with chronic heart failure

Impairment of endothelium-dependent vasodilation has recently been reported in the peripheral vascular bed in patients with chronic heart failure. However, the clinical implications of this type of vascular dysfunction have yet to be elucidated. We have determined the degree of impairment of endothelium-dependent vasodilation as evaluated by acetylcholine-induced changes in forearm blood flow and compared this to various clinical parameters in 23 patients with chronic heart failure. Cumulative changes in forearm blood flow induced by acetylcholine (3.0 and 4.5 micrograms/min/dl tissue volume) were significantly lower in patients with chronic heart failure than in normal controls (10.1 +/- 8.0 ml/min/100 ml vs 20.4 +/- 11.7 ml/min/100 ml tissue volume; p < 0.01). In patients with heart failure, no significant relation was found between acetylcholine-induced changes in forearm blood flow and age, sex, duration of symptoms, duration of hospital stay, or resting hemodynamic parameters, although a significant positive correlation was observed with peak oxygen uptake (r = 0.53, p < 0.05) and ventilatory threshold (r = 0.42, p < 0.05). These observations suggest that the impairment of endothelium-dependent peripheral vasodilation may be one of the factors contributing to exercise intolerance in patients with chronic heart failure, probably resulting from its limiting effect on nutritive skeletal muscle blood flow during exercise.

Parathyroid hormone-related protein reduces cytosolic free Ca2+ level and tension in rat aortic smooth muscle

The effect of parathyroid hormone-related protein (PTHrP) on cytosolic free Ca2+ level ([Ca2+]i) and tension in rat aortic smooth muscle was investigated with special reference to the role of production and action of cyclic AMP. Rat aortic spiral strip preparations without endothelium were treated with the acetoxymethyl ester of fura 2, and the ratio of fluorescences (R340/380), an index of [Ca2+]i, emitted from smooth muscle, was measured. The tension of the preparations was simultaneously measured. PTHrP-(1-34) produced concentration-dependent decreases both in the tension and in R340/380 increased by phenylephrine (10(-7) M). These effects were significantly inhibited by pretreatment with either PTHrP-(7-34) (10(-6) M), a PTHrP receptor antagonist, or with Rp diastereomer of adenosine cyclic 3',5'-phosphorothioate (RpcAMPS; 10(-4) M), a cyclic AMP-dependent protein kinase inhibitor. Dibutyryl cyclic AMP (10(-5)-10(-3.5 M) elicited effects similar to those of PTHrP-(1-34). PTHrP-(1-34) was found to significantly elevate aortic cAMP level, measured by specific radioimmunoassay, after 5 min incubation with PTHrP-(1-34). These results suggest that the decrease in [Ca2+]i is involved in the vasodilator action of PTHrP, and that the decreases both in tension and in [Ca2+]i might be attributed to cyclic AMP production stimulated by PTHrP.

Protection against cisplatin lethality and renal toxicity by chlorpromazine in mice

The effect of chlorpromazine on acute lethal toxicity and nephrotoxicity induced by cisplatin was studied in mice. Chlorpromazine (i.p.) given 1 h before cisplatin greatly reduced lethal and renal toxicities of cisplatin, while chlorpromazine did not reduce the antitumor activity of cisplatin against sarcoma 180 in ddY mice or El-4 leukemia in C57BL/6J mice.

Isolation of an ascitic oncodevelopmental protein exhibiting high sequence homology with calcium-binding protein MRP8

A human oncodevelopmental protein (ODP) with a molecular size of 28 kDa was isolated, employing malignant ascitic fluid of an advanced mixed mesodermal tumor of the uterus, by anti-ODP coupled Affi-Gel 10 column chromatography, followed by preparative PAGE. The final preparation obtained with this procedure gave a single band exhibiting reactivity with an anti-ODP antibody on analytical sodium dodecyl sulfate-PAGE. The sequence of the first 20 N-terminal amino acids of this protein is identical with those of both the cystic fibrosis protein and Ca-binding protein MRP8 except at position 17, for which no result was obtained. Sequence analysis suggested that the protein shows 90% sequence homology with both these proteins.

Seroepidemiological studies of bovine babesiosis caused by Babesia ovata, B. bigemina and B. bovis in Peninsular Malaysia

Cattle in Peninsular Malaysia were examined for evidence of infection with Babesia ovata, B. bigemina and B. bovis by an enzyme-linked immunosorbent assay for detection of antibody to the three Babesia species. All of the test samples when assayed with B. ovata antigen, resulted in low value indicating low probability of cattle infected with B. bigemina, 74.4% were positive for B. bovis and 72.6% were positive for both Babesia species. In addition, a serological survey with regard to age difference was carried out on a milk production farm. High reactivity antibody to B. bigemina and B. bovis was detected in calves less than 1 month of the age. The reactivity decreased in calves 1-3 months of the age. Then, the reactivity increased for both Babesia species in 6 months old calves. These results suggested that cattle infected with B. bigemina and B. bovis were widespread throughout Peninsular Malaysia and that both parasites might exist as an enzootical parasite.

Monoclonal antibody specifically reacting against 73-kilodalton heat shock cognate protein: possible expression on mammalian cell surface

The heat shock proteins (hsp) are regarded as being immunogenic to the animal hosts. Although certain hsp are suggested to be expressed on the cell surface, further evidence for the cell surface expression of these proteins has been required. In this article we report the development of a MAb NT22. This antibody reacted with ATP-binding proteins (which contain a large amount of 70-kDa hsp family) of HeLa cells, and with purified bovine 70-kDa hsp. It did not react with the E. coli lysate, but clearly reacted with the recombinant rat hsc73. However, NT22 failed to react with hsp72. Furthermore, stress treatment of cells also indicated that considerable amounts of NT22-defined antigen translocated into the nucleus from the cell cytoplasm. These results suggest that NT22 is a novel MAb that reacts specifically to the mammalian hsc73. Moreover, this antibody could detect the constitutive and stress-induced cell surface expression of its relevant antigen. It is expressed preferentially on EBV-transformed B cell and certain epithelial cancer cell lines. However, resting B cells did not express this antigen on the cell surface. These data indicate that hsc73 could be expressed on the cell surface of certain cells, and suggest that hsc73 may interact with the host immune system.

Giant symptomatic myelolipoma of the adrenal gland

A case of giant symptomatic myelolipoma is described in which clinical differentiation was difficult. It was considered to be an extremely rare case of giant myelolipoma arising in the adrenal gland. Histologically the present case contained more lipomatous elements than others reported to data. This is a case of giant adrenal myelolipoma with a few foci of myeloid elements and it is suggested that this case has a true neoplastic nature rather than a hyperplastic or metaplastic one.