Characterization of nanoscale mechanical heterogeneity in a metallic glass by dynamic force microscopy

We report nanoscale mechanical heterogeneity of a metallic glass characterized by dynamic force microscopy. Apparent energy dissipation with a variation of ~12%, originating from nonuniform distribution of local viscoelasticity, was observed. The correlation length of the heterogeneity was measured to be ~2.5 nm, consistent with the dimension of shear transformation zones for plastic flow. This study provides the first experimental evidence on the nanoscale viscoelastic heterogeneity in metallic glasses and may fill the gap between atomic models and macroscopic glass properties.

HPLC Retention time prediction for metabolome analysi

Liquid Chromatography Time-of-Flight Mass Spectrometry (LC-TOF-MS) is widely used for profiling metabolite compounds. LC-TOF-MS is a chemical analysis technique that combines the physical separation capabilities of high-pressure liquid chromatography (HPLC) with the mass analysis capabilities of Time-of-Flight Mass Spectrometry (TOF-MS) which utilizes the difference in the flight time of ions due to difference in the mass-to-charge ratio. Since metabolite compounds have various chemical characteristics, their precise identification is a crucial problem of metabolomics research. Contemporaneously analyzed reference standards are commonly required for mass spectral matching and retention time matching, but there are far fewer reference standards than there are compounds in the organism. We therefore developed a retention time prediction method for HPLC to improve the accuracy of identification of metabolite compounds. This method uses a combination of Support Vector Regression and Multiple Linear Regression adaptively to the measured retention time. We achieved a strong correlation (correlation coefficient = 0.974) between measured and predicted retention times for our experimental data. We also demonstrated a successful identification of an E. coli metabolite compound that cannot be identified by precise mass alone.

Cloning and expression of cDNA for salmon growth hormone in Escherichia coli

cDNA clones encoding chum salmon (Oncorhynchus keta) growth hormone (sGH) have been isolated from a cDNA library prepared from chum salmon pituitary gland poly(A)(+) RNA. Synthetic oligodeoxynucleotide mixtures based on amino acid residues 23-28 of sGH were used as hybridization probes to select recombinant plasmids carrying the sGH coding sequence. The complete nucleotide sequence of sGH cDNA has been determined. The cDNA sequence codes for a polypeptide of 210 amino acids, including a putative signal sequence of 22 amino acids. The 5' and 3' untranslated regions of the message were 64 and 426 bases long, respectively. Mature sGH was efficiently expressed in Escherichia coli carrying a plasmid in which the sGH cDNA was under control of the E. coli trp promoter; sGH comprised about 15% of the total cellular protein in such bacteria. The partially purified sGH from E. coli stimulated the growth of rainbow trout and the activity was indistinguishable from that of natural sGH.

Complete genome sequence and comparative analysis of Shewanella violacea, a psychrophilic and piezophilic bacterium from deep sea floor sediments

Remineralization of organic matter in deep-sea sediments is important in oceanic biogeochemical cycles, and bacteria play a major role in this process. Shewanella violacea DSS12 is a psychrophilic and piezophilic gamma-proteobacterium that was isolated from the surface layer of deep sea sediment at a depth of 5110 m. Here, we report the complete genome sequence of S. violacea and comparative analysis with the genome of S. oneidensis MR-1, isolated from sediments of a freshwater lake. Unlike S. oneidensis, this deep-sea Shewanella possesses very few terminal reductases for anaerobic respiration and no c-type cytochromes or outer membrane proteins involved in respiratory Fe(iii) reduction, which is characteristic of most Shewanella species. Instead, the S. violacea genome contains more terminal oxidases for aerobic respiration and a much greater number of putative secreted proteases and polysaccharases, in particular, for hydrolysis of collagen, cellulose and chitin, than are encoded in S. oneidensis. Transporters and assimilatory reductases for nitrate and nitrite, and nitric oxide-detoxifying mechanisms (flavohemoglobin and flavorubredoxin) are found in S. violacea. Comparative analysis of the S. violacea genome revealed the respiratory adaptation of this bacterium to aerobiosis, leading to predominantly aerobic oxidation of organic matter in surface sediments, as well as its ability to efficiently use diverse organic matter and to assimilate inorganic nitrogen as a survival strategy in the nutrient-poor deep-sea floor.

Complete genome sequence and comparative analysis of Shewanella violacea, a psychrophilic and piezophilic bacterium from deep sea floor sediments

Remineralization of organic matter in deep-sea sediments is important in oceanic biogeochemical cycles, and bacteria play a major role in this process. Shewanella violacea DSS12 is a psychrophilic and piezophilic gamma-proteobacterium that was isolated from the surface layer of deep sea sediment at a depth of 5110 m. Here, we report the complete genome sequence of S. violacea and comparative analysis with the genome of S. oneidensis MR-1, isolated from sediments of a freshwater lake. Unlike S. oneidensis, this deep-sea Shewanella possesses very few terminal reductases for anaerobic respiration and no c-type cytochromes or outer membrane proteins involved in respiratory Fe(iii) reduction, which is characteristic of most Shewanella species. Instead, the S. violacea genome contains more terminal oxidases for aerobic respiration and a much greater number of putative secreted proteases and polysaccharases, in particular, for hydrolysis of collagen, cellulose and chitin, than are encoded in S. oneidensis. Transporters and assimilatory reductases for nitrate and nitrite, and nitric oxide-detoxifying mechanisms (flavohemoglobin and flavorubredoxin) are found in S. violacea. Comparative analysis of the S. violacea genome revealed the respiratory adaptation of this bacterium to aerobiosis, leading to predominantly aerobic oxidation of organic matter in surface sediments, as well as its ability to efficiently use diverse organic matter and to assimilate inorganic nitrogen as a survival strategy in the nutrient-poor deep-sea floor.

A reporter assay for G-protein-coupled receptors using a B-cell line suitable for stable episomal expression

We have established a cAMP response element (CRE)-mediated reporter assay system for G-protein-coupled receptors (GPCRs) using an oriP-based estrogen-inducible expression vector and the B-cell line (GBC53 or GBCC71) that expresses EBNA-1 and is adapted to serum-free culture. GBC53 harbors a GAL4-ER expression unit and a CRE-luciferase gene in the genome, and GBCC71 also harbors expression units for two chimeric Galphas proteins (Gs/q and Gs/i). Introduction of a GPCR expression plasmid into GBC53 or GBCC71 creates polyclonal stable transformants in 2 weeks, and these are easily expanded and used for assays after induction of the GPCR expression. Using GBC53, we detected ligand-dependent signals of Gs-coupled GPCRs such as glucagon-like peptide 1 receptor (GLP1R) and beta2 adrenergic receptor (beta2AR) with high sensitivity. Interestingly, we also detected constitutive activity of beta2AR. Using GBCC71, we detected ligand-dependent signals of Gq- or Gi-coupled GPCRs such as H1 histamine receptor and CXCR1 chemokine receptor in addition to Gs-coupled GPCRs. An agonist, antagonist, or inverse agonist was successfully evaluated in this system. We succeeded in constructing a 384-well high-throughput screening (HTS) system for GLP1R. This system enabled us to easily and rapidly make a large number of efficient GPCR assay systems suitable for HTS as well as ligand hunting of orphan GPCRs.

Characterization of orphan monooxygenases by rapid substrate screening using FT-ICR mass spectrometry

Characterization of orphan enzymes, for which the catalytic functions and actual substrates are still not elucidated, is a significant challenge in the postgenomic era. Here, we describe a general strategy for exploring the catalytic potentials of orphan monooxygenases based on direct infusion analysis by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS). Eight cytochromes P450 from Bacillus subtilis were recombinantly expressed in Escherichia coli and subjected to a reconstitution system containing appropriate electron transfer components and many potential substrates. The reaction mixtures were directly analyzed using FT-ICR/MS, and substrates of the putative enzymes were readily identified from the mass spectral data. This allowed identification of previously unreported CYP109B1 substrates and the functional assignment of two putative cytochromes P450, CYP107J1 and CYP134A1. The FT-ICR/MS-based approach can be easily applied to large-scale screening with the aid of the extremely high mass resolution and accuracy.

Intra-operative natural sound decreases salivary amylase activity of patients undergoing inguinal hernia repair under epidural anesthesia

BACKGROUND

The perioperative period is psychologically as well as physically stressful for patients. Although music and sound are known to reduce patients' psychological stress, a few previous studies showed an objective outcome of music. The aim of the present study was to evaluate the relaxing effect of music during epidural anesthesia, using patients' salivary amylase activity.

METHODS

Thirty-two American Society of Anesthesiologists (ASA) I or II patients presenting for inguinal hernia repair under epidural anesthesia were randomly assigned to listen to sounds of a soft wind and a twitter (S group) or to have no sounds (N group). Patients' salivary amylase activity was evaluated on arrival to the operating room and at wound closure.

RESULTS

Intra-operative music significantly decreased salivary amylase activity at wound closure in the S group and the activity at wound closure of the S group was significantly smaller than that of the N group.

CONCLUSION

Intra-operative natural sound significantly decreased salivary amylase activity of patients undergoing inguinal hernia repair under epidural anesthesia.

GeneLook: a novel ab initio gene identification system suitable for automated annotation of prokaryotic sequences

With the rapid increases in the amounts of sequence data for prokaryotic genomes, it has become important to develop systems for automated and accurate genome annotation. We present herein a novel ab initio gene identification system, GeneLook, that predicts protein-coding open reading frames (ORFs) with high sensitivity and specificity with no prior knowledge of the sequence composition. The system predicts protein-coding ORFs in two stages, seed ORF selection and main prediction. In the selection of reliable seed ORFs containing at least 200 codons, GeneLook predicts translation start sites and operon structures through searches for ribosome-binding sites and a novel operon prediction algorithm. The codon and nucleotide frequencies of seed ORFs are then used to determine values for two new coding-potential parameters for identification of protein-coding ORFs of at least 34 codons and for another parameter that improves the prediction accuracy for GC-rich genomes. In the main prediction, GeneLook uses these parameters to identify the most likely genes of a given minimal length. We assessed the performance of GeneLook with two indices, sensitivity and specificity that are defined as true positives (TP)/(TP+false negatives) and TP/(TP+false positives), respectively. This system predicted protein-coding ORFs for Escherichia coli and Bacillus subtilis with sensitivities of 96.5% and 96.2%, respectively, and specificities of 96.9% and 96.1%, respectively. The system also identified 94.1% of annotated genes of the Pseudomonas aeruginosa genome, which is GC-rich, with high specificity (97.2%). Furthermore, GeneLook identified protein-coding ORFs with high accuracy from a wide variety of prokaryotic genomes.

Involvement of apoptosis in syncytial cell death induced by canine distemper virus

The Yanaka strain, a field isolate of Canine distemper virus (CDV), caused extensive syncytial cytopathic effects (CPEs) followed by cell death in vitro. Syncytium formation is an important aspect of CDV pathogenicity, but the mechanism of the fusion-induced cell death is still not understood. In this study, the involvement of apoptosis in the CDV-induced CPE was investigated. We also examined apoptosis in cells infected with a persistent strain of CDV, the Yanaka-BP strain derived from the Yanaka strain, because this strain does not cause obvious CPE. DNA laddering together with Terminal transferase dUTP nick endlabeling (TUNEL) assay indicated that the Yanaka strain infection, but not the Yanaka-BP infection induced apoptosis. In addition, flow cytometric analysis similarly indicated that the Yanaka-BP strain induced apoptosis significantly less frequently than the Yanaka strain did. Thus, absence of apoptosis may be implicated in the CPE and establishment of persistent CDV infection.

In vivo transfer of a neuronal nitric oxide synthase expression vector into the rat bladder by electroporation

OBJECTIVE

To investigate the possibility of in vivo gene transfer by attempting to transfer the neuronal nitric oxide synthase (nNOS) gene into rat bladder using electroporation.

MATERIALS AND METHODS

The bladder was exposed through an abdominal midline incision in 8-week-old male rats. Plasmid DNA of the marker genes green fluorescent protein (GFP) and luciferase, and the nNOS gene, was then injected into the subserosal space of the bladder and electroporation applied. At 72 h after gene transfer, GFP and luciferase were assayed in the isolated bladder and immunohistochemical staining used to detect nNOS; NO(x) released from isolated bladder strips was also assessed using microdialysis and high-performance liquid chromatography.

RESULTS

From the luciferase assay, 45 V, 1 Hz, 50 ms and eight pulses were selected as the optimum conditions for electroporation. Bladder specimens with GFP genes injected by electroporation showed bright and numerous sites of GFP expression in the smooth muscle layer. In rats with the nNOS gene injected by electroporation there was marked nNOS immunoreactivity, and NO(x) released from bladder strips was significantly greater than in the control groups.

CONCLUSIONS

These results suggest that electroporation is a useful technique for in vivo gene transfer into rat bladder smooth muscles, and that the nNOS gene transferred by this procedure functionally expresses and contributes to NO production.

Formation of advanced tokamak plasmas without the use of an ohmic-heating solenoid

A new operational scenario of advanced tokamak formation was demonstrated in the JT-60U tokamak. This was accomplished by electron cyclotron and lower hybrid waves, neutral beam injection, and the loop voltage supplied by the vertical field and shaping coils. The Ohmic heating (OH) solenoid was not used but a small inboard coil (part of the shaping coil), providing less than 20% of total poloidal flux, was used. The plasma thus obtained had both internal and edge transport barriers, with an energy confinement time of 1.6 times H-mode scaling, a poloidal beta of 3.6, and a normalized beta of 1.6, and a large bootstrap current fraction (>90%). This result opens up a possibility to reduce, and eventually eliminate, the OH solenoid from a tokamak reactor, which will greatly improve its economic competitiveness.

Complete sequencing and characterization of 21,243 full-length human cDNAs

As a base for human transcriptome and functional genomics, we created the "full-length long Japan" (FLJ) collection of sequenced human cDNAs. We determined the entire sequence of 21,243 selected clones and found that 14,490 cDNAs (10,897 clusters) were unique to the FLJ collection. About half of them (5,416) seemed to be protein-coding. Of those, 1,999 clusters had not been predicted by computational methods. The distribution of GC content of nonpredicted cDNAs had a peak at approximately 58% compared with a peak at approximately 42%for predicted cDNAs. Thus, there seems to be a slight bias against GC-rich transcripts in current gene prediction procedures. The rest of the cDNAs unique to the FLJ collection (5,481) contained no obvious open reading frames (ORFs) and thus are candidate noncoding RNAs. About one-fourth of them (1,378) showed a clear pattern of splicing. The distribution of GC content of noncoding cDNAs was narrow and had a peak at approximately 42%, relatively low compared with that of protein-coding cDNAs.

Inhibitory effects of Helicobacter pylori infection on murine autoimmune gastritis

BACKGROUND AND AIM

Long term Helicobacter pylori infection leads to atrophic gastritis but the relation between H pylori infection and autoimmune related atrophic gastritis (AIG) remains unclear. We studied the effects of H pylori infection on the pathophysiology of AIG in mice.

MATERIALS AND METHODS

BALB/c nu/nu mice (n=40) with or without H pylori infection received splenocytes from neonatally thymectomised mice to induce AIG. Half of the mice were orally infected with H pylori prior to AIG induction. Histological findings, and local and systemic immune responses were serially evaluated.

RESULTS

Two and six months after transfer, parietal cells in uninfected mice were depleted while those in infected mice were well preserved. The degree of gland atrophy (p<0.01), hyperplasia (p<0.01), gastric pH (p<0.05), and serum gastrin levels of infected mice were significantly lower than those of uninfected mice. Serum antiparietal cell antibody levels gradually decreased in infected mice, and were significantly lower than those of uninfected mice at six months (p<0.05). Real time polymerase chain reaction studies revealed significantly higher interleukin 4 (p<0.05) and transforming growth factor beta (p<0.05) gene expression in the gastric mucosa in infected mice than in uninfected mice at both two and six months after AIG induction.

CONCLUSIONS

H pylori infection inhibited the development of AIG in mice. Th2-type immune responses and transforming growth factor beta in the gastric microenvironment might be involved in the inhibitory effects of H pylori infection on the development of AIG, in which Th1-type responses have an important role.

[Non-compromised grafting policy in off-pump coronary artery bypass]

BACKGROUND

The off-pump coronary artery bypass (OPCAB) has been prevalent around the world. However the most optimal selection of graft conduits has still been controversial.

METHODS

Between January 2002 and April 2003, 126 consecutive isolated coronary artery bypass procedures were attempted to performed without cardiopulmonary bypass. A mean age of the patients was 69.3 (47-90). Fifteen patients were operated on emergently and 16 were urgently, including 15 patients requiring preoperative intra-aortic balloon pumping (IABP). Five patients underwent reoperative coronary bypass.

RESULTS

All procedures were completed without cardiopulmonary bypass. The mean number of grafts per patient was 3.23 (range, 1 to 6). The skeletonized arterial conduits were aggressively used [117 left internal mammary artery (LIMA) to 155 sites, 70 right internal mammary artery (RIMA) to 79 sites, 57 right gastro-epiploic artery (RGEA) to 82 sites and 49 saphenous vein (SV) to 91 sites]. Cardiac-related hospital mortality was none. Angiographic assessment of grafts demonstrated that patency of LIMA, RIMA, RGEA and SV were 98.6%, 100%, 100%, and 97.6% respectively.

CONCLUSION

OPCAB with skeletonized in situ arterial conduits is secure and feasible.