Resuspension of DNA sequencing reaction products in agarose increases sequence quality on an automated sequencer

We are investigating approaches to increase DNA sequencing quality. Since a majorfactor in sequence generation is the cost of reagents and sample preparations, we have developed and optimized methods to sequence directly plasmid DNA isolated from alkaline lysis preparations. These methods remove the costly PCR and post-sequencing purification steps but can result in low sequence quality when using standard resuspension protocols on some sequencing platforms. This work outlines a simple, robust, and inexpensive resuspension protocol for DNA sequencing to correct this shortcoming. Resuspending the sequenced products in agarose before electrophoresis results in a substantial and reproducible increase in sequence quality and read length over resuspension in deionized water and has allowed us to use the aforementioned sample preparation methods to cut considerably the overall sequencing costs without sacrificing sequence quality. We demonstrate that resuspension of unpurified sequence products generated from template DNA isolated by a modified alkaline lysis technique in low concentrations of agarose yields a 384% improvement in sequence quality compared to resuspension in deionized water. Utilizing this protocol, we have produced more than 74,000 high-quality, long-read-length sequences from plasmid DNA template on the MegaBACET 1000 platform.

A case of well-differentiated minute hepatocellular carcinoma with extrahepatic metastasis

A rare case of well-differentiated minute hepatocellular carcinoma (HCC) metastasizing to distant sites in a 77-year-old man with hepatitis C virus (HCV)-related cirrhosis is presented. Ultrasonography (US) disclosed a 9 mm hypoechoic lesion in segment seven (S7) of the liver, although computed tomography (CT), magnetic resonance imaging (MRI) and angiography did not reveal any space-occupying lesion. Ultrasound-guided biopsy showed the histological features of well-differentiated HCC. A plain film of the abdomen and CT revealed osteolytic changes in the sacrum and the lumbar vertebra. Ultrasound-guided biopsy of the sacrum revealed well-to-moderately differentiated HCC metastasizing from the liver. Percutaneous ethanol injection therapy (PEIT) effected complete response and completely eliminated the abnormal findings on US. Three months after PEIT, metastasis to the thoracic vertebra was revealed by CT, despite negative alpha-fetoprotein-mRNA in serum. This is the first report describing a well-differentiated HCC with metastatic potential. Further studies may provide insights into metastasis of well-differentiated HCC.

Functional analysis of vif genes derived from various primate immunodeficiency viruses

Replication property in cells of human and simian immunodeficiency viruses (HIVs and SIVs) lacking intact vif gene was evaluated. Of 10 vif mutants constructed in vitro of the major four HIV/SIV groups, only those derived from HIV-1 and HIV-2/SIVmac displayed replication defect. The cell lines non-permissive for the vif mutants of HIV-1 and SIVmac were found to be different. To determine whether Vif is exchangeable between HIV-1 and SIVmac, chimeric virus clones with respect to the vi gene were constructed and virus replication in the cells non-permissive for the vif mutant viruses was monitored. Productive infection in these cells of chimeric viruses clearly indicated that Vif is functionally exchangeable, and that Vifs of different virus origin act through a similar mechanism.

Effect of pulsed output ultrasound on the transdermal absorption of indomethacin from an ointment in rats

The effect of pulsed output ultrasound (1 MHz) with on/off ratios of 1:2, 1:4 and 1:9 on transdermal absorption of indomethacin from an ointment was studied in rats. Ultrasound energy was supplied for between 10 and 19 min at a range of intensities (1.0-2.5 W.cm-2), energy levels commonly used for therapeutic purposes. The on/off pulsed ratio, intensity and the time of application were found to play an important role in the transdermal phonophoretic delivery system of indomethacin; 1:2 pulsed output ultrasound appeared to be the most effective in improving the transdermal absorption. The highest penetration was observed at an intensity of 1.0 W.cm-2 and application time of 15 min. With pulsed output it was possible to use higher intensities of ultrasound without increasing skin temperature or damaging skin.

Antiviral activity of lignans and their glycosides from Justicia procumbens

Ten antiviral lignans, seven known (justicidins A, B, C and D, diphyllin, diphyllin apioside and diphyllin apioside-5-acetate) and three new compounds, justicidinosides A (justicidin C 6'-O-glucoside), B (justicidin A 6'-O-glucoside) and C (justicidin B 6'-O-glucoside), were isolated from a methanolic extract of the aerial parts of Justicia procumbens var. leucantha. Justicidins A and B, diphyllin, diphyllin apioside and diphyllin apioside-5-acetate showed strong antiviral activity (the MIC were less than 0.25 microgram ml-1, respectively) against vesicular stomatitis virus and low cytotoxicity (the MTC were larger than 31 micrograms ml-1, respectively) against cultured rabbit lung cells (RL-33).

Cytotoxic xanthones from Garcinia hanburyi

Eleven novel cytotoxic xanthones, gambogin, morellin dimethyl acetal, isomoreollin B, moreollic acid, gambogenic acid, gambogenin, isogambogenin, desoxygambogenin, gambogenin dimethyl acetal, gambogellic acid and hanburin were isolated together with four known xanthones, gambogic acid, isomorellin, morellic acid and desoxymorellin, from the dry latex of Garcinia hanburyi. The structures were elucidated by a detailed spectroscopic analysis.

Effects of erucic acid therapy on Japanese patients with X-linked adrenoleukodystrophy

Ten Japanese boys with childhood adrenoleukodystrophy (ALD), one adult patient with adrenomyeloneuropathy (AMN), and two presymptomatic ALD boys were treated with dietary erucic acid (C22:1) for more than 12 months; except in a case of childhood ALD patient who died 7 months after beginning erucic acid therapy. During erucic acid therapy, the serum levels of very long-chain fatty acid (VLCFA) (C24:0/C22:0) decreased within 1-2 months in all patients, and these levels in four of the patients decreased to the normal range. Neurological examination and MRI findings in all 10 of the childhood ALD patients showed progression of the disease while they were receiving the dietary therapy. However, the mean interval between the onset of awkward gait and a vegetative state in diet-treated patients was significantly longer than that in the untreated patients. One AMN patient showed slight improvement of spastic gait and lessened pain in the lower limbs due to spasticity. The two presymptomatic ALD boys remained intact on clinical examination and on MRI findings for 38 and 23 months, respectively, after starting the diet.

Thyroid cancer in a case with the Alagille syndrome

A 19-year-old woman with the Alagille syndrome developed papillary thyroid carcinoma with lung metastasis. She was diagnosed as having Alagille syndrome at the age of 8. Following total thyroidectomy and lymph nodes dissection, iodine-131 therapy was conducted for local and distant metastases. This is the first report of a case of thyroid cancer accompanying Alagille syndrome.

Balanced complex rearrangement involving chromosomes 8, 9, and 12 in a normal mother, derivative chromosome 9 with recombinant chromosome 12 in her daughter with minor anomalies

We report on a 19-month-old girl with a derivative chromosome 9 and a recombinant chromosome 12 resulting from a maternal balanced complex rearrangement involving chromosomes 8, 9, and 12. The karyotype of the phenotypically normal mother was 46,XX,t(8;12) (9;12) (8qter-->8p23::12q12-->12q 15::9q32-->9qter;9pter-->9q32::12q15--> 12qter; 12pter-->12q12::8p23-->8pter). The child's karyotype was 46,XX,-9,-12, +der(9) (9pter-->9q32::12q15-->12qter), +rec(12) (12pter-->12q15::9q32-->9qter) mat. The child had severe growth retardation, minor anomalies including trigonocephaly, hypertelorism, broad nasal root, apparently low-set and posteriorly angulated ears, triangular face, pectus carinatum, clinodactyly of fifth fingers, and almost normal psychomotor development. To the best of our knowledge, there have been only 3 previous reports of recombination derived from parental complex chromosome rearrangements. In the recombination products, the chromosomes were apparently balanced and the offspring had no clinical abnormalities. The present case exhibited abnormalities and may have a submicroscopic aberration of 12q arising from crossing over during maternal meiotic pairing, although her chromosomes appeared to be balanced.

Improvement of clinical and MRI findings in a boy with adrenoleukodystrophy by dietary erucic acid therapy

A 5-year-old boy with adrenoleukodystrophy, with clinical symptoms of visual, mental and motor disturbances which progressed rapidly, was treated with Lorenzo's oil consisting 1 volume of glyceryl trierucate and 4 volumes of glyceryl trioleate. Five months after initiation of this therapy, ability to swallow was enhanced and T2-weighted magnetic resonance imaging of the brain revealed regression of high intensity area of the parieto-occipital white matter.

Gene deletions in Japanese patients with Duchenne and Becker muscular dystrophies: deletion study and carrier detection

Fifty unrelated Japanese patients with Duchenne and Becker muscular dystrophy (DMD and BMD) have been studied through use of the dystrophin cDNA probes. The 14-kb dystrophin cDNA was subdivided into six subclones, and Hind III-digested DNAs were analyzed by Southern blotting. Of 50 unrelated patients, 20 showed a deletion of one or several of the exon-containing Hind III fragments (40.0%). These corresponded to 50% (11/22) of BMD patients and 32.1% (9/28) of DMD patients, and the position and extent of deletions were mapped and proven to be more heterogeneous in DMD than in BMD. Both ends of deletions detected by probe 1-2a were common to all six BMD patients, and the 5' ends of deletions in probe 5b-7 were also common to four BMD patients. The phenotypic-specific deletion in Japanese BMD patients existed in the 5' end of the DMD gene, although an apparently similar deletion produced a wide range of clinical courses (BMD phenotype). Three out of eight females in DMD/BMD families were diagnosed as carriers through use of the junctional fragment and dosage analyses of dystrophin cDNA.

[CT findings and prognoses of anoxic brain damage due to near-drowning in children]

We investigated the relationship between serial cranial CT findings and prognoses in 11 children after near-drowning. These patients were rescued after heart arrest for more than 10 minutes and all comatose on admission. CT scans were performed within 2 weeks, at 3 weeks-1 month, 2-4 months and more than 5 months after admission. Characteristics of CT findings and prognoses were classified into four groups. Group 1: low density areas in thalami, basal ganglia and cortical white matters within 2 weeks (three cases; one died, two became vegetative). Group 2: enlargement of the third ventricle at 3 weeks-1 month, and atrophy of pons at 2-4 months (three cases; severe quadriplegia and mental retardation). Group 3: enlargement of the third ventricle at 3 weeks-1 month, but atrophy of pons not observed at 2-4 months (three cases; mild motor disabilities and mild mental retardation). Group 4: enlargement of third ventricle not observed at 3 weeks-1 month (two cases; neither paralysis nor mental retardation).

Gene deletions in Japanese patients with Duchenne and Becker muscular dystrophy

Thirty-eight unrelated Japanese patients with Duchenne and Becker muscular dystrophy (DMD and BMD) have been investigated with the DMD cDNA probes. The 14-kb DMD cDNA was subdivided into 6 subclones and HindIII-digested DNAs were analyzed by Southern blotting. Out of 38 unrelated patients, 14 showed a deletion of one or several of the exon-containing HindIII fragments (36.8%). These corresponded to 50% (9/18) of BMD patients and 25% (5/20) of DMD patients, and the position and extent of deletions were mapped and proved to be more heterogeneous in DMD than in BMD. Both ends of deletions detected in probe 1-2a were common to all six BMD patients without the maintenance of reading frame of messenger RNA, and 5' ends of deletions in probe 5b-7 were also common but maintained in frame in three BMD patients. The phenotypic-specific deletion in Japanese BMD patients has existed in the 5' end of the DMD gene, although its apparently similar deletion produced a wide range of clinical courses (BMD phenotype). There was no tight correlation between clinical severity and presence or absence of deletion in DMD or BMD.

[Prevention of postoperative infection following cardiac catheterization in pediatric field. Study of air-borne bacteria in X-ray room and evaluation of an antibiotic used for prevention of postoperative infection]

As part of preventive measures against postoperative infection following cardiac catheterization in infants with cardiac diseases, especially falling bacteria in X-ray room was studied. Moreover, a synthetic penicillin, ticarcillin (TIPC), was used as preventive antibiotic against postoperative infections due to falling bacteria which probably contaminate the air in the X-ray examination room, and the efficacy and side effects of the drug were observed. As result, coagulase-negative Staphylococcus was detected the most, followed by Micrococcus and then by fungus. The number of these 3 organisms corresponded to 90.3% of the total number of falling bacteria detected during operation. The number of falling bacteria during operation was 5.1 times larger than that before operation. Taking into account normal flora of skin, falling bacteria present in the X-ray room and causative organisms of bacterial endocarditis, TIPC was administered to 30 cases intravenously 5 times at a dose of 30 mg/kg every 8 hours for the purpose of preventing possible postoperative infections following cardiac catheterization. The drug was effective to prevent such infections in all cases. No side effects were noted in any case, in peripheral blood and hepatic function tests and other observations.

Antibiotic resistance of indole-positive Klebsiella pneumoniae

Resistance patterns to antibiotics differed markedly between indole-positive and indole-negative Klebsiella pneumoniae strains. Multiple-drug-resistant strains were almost exclusively indole-negative. Ampicillin and kanamycin resistances in the indolepositive strains tested were not transmissible, whereas many of those resistances in the indole-negative strains were transmissible, together with other drug resistances to an Escherichia coli recipient. The substrate profile of the beta-lactamase from the indole-positive strains was fairly different from that of the beta-lactamase mediated by the ampicillin resistance plasmid.