Genomic and proteomic characterization of the large Myoviridae bacteriophage ϕTMA of the extreme thermophile Thermus thermophilus

A lytic phage, designated as ϕTMA, was isolated from a Japanese hot spring using Thermus thermophilus HB27 as an indicator strain. Electron microscopic examination showed that ϕTMA had an icosahedral head and a contractile tail. The circular double-stranded DNA sequence of ϕTMA was 151,483 bp in length, and its organization was essentially same as that of ϕYS40 except that the ϕTMA genome contained genes for a pair of transposase and resolvase, and a gene for a serine to asparagine substituted ortholog of the protein involved in the initiation of the ϕYS40 genomic DNA synthesis. The different host specificities of ϕTMA and ϕYS40 could be explained by the sequence differences in the C-terminal regions of their distal tail fiber proteins. The ΔpilA knockout strains of T. thermophilus showed simultaneous loss of sensitivity to their cognate phages, pilus structure, twitching motility and competence for natural transformation, thus suggesting that the phage infection required the intact host pili. Pulsed-field gel electrophoresis analysis of the ϕTMA and ϕYS40 genomes revealed that the length of their DNA exceeded 200 kb, indicating that the terminal redundancy is more than 30% of the closed circular form. Proteomic analysis of the ϕTMA virion using a combination of N-terminal sequencing and mass spectrometric analysis of peptide fragments suggested that the maturation of several proteins involved in the phage assembly process was mediated by a trypsin-like protease. The gene order of the phage structural proteins was also discussed.

Calditerricola satsumensis gen. nov., sp. nov. and Calditerricola yamamurae sp. nov., extreme thermophiles isolated from a high-temperature compost

Two novel thermophilic micro-organisms, designated YMO81T and YMO722T, were isolated from a high-temperature compost (internal temperature >95 °C). The isolates were able to grow at 80 °C in a nutrient broth and in a synthetic medium. Cells were aerobic, Gram-negative rods (0.3×4.0 μm). Spore formation was not observed. Strain YMO81T grew at 83 °C and pH 6.9–8.9 and grew optimally at 78 °C and pH 7.5 with 2 % NaCl. For growth in a synthetic minimal medium at 70 °C, the vitamins biotin, folic acid and thiamine and the amino acids glutamine and methionine were essential for growth of both strains; at 80 °C, strain YMO81T also required histidine, isoleucine, leucine, lysine, phenylalanine, serine, tryptophan and valine. Cellular fatty acids of the isolates comprised mainly iso-C17 : 0 and anteiso-C17 : 0. The DNA G+C contents of strains YMO81T and YMO722T were 70 and 64 mol%, respectively. When the 16S rRNA gene sequences of the isolates were compared with those of other bacteria, highest similarity was observed with Planifilum yunnanense LA5T (90 % 16S rRNA gene sequence similarity). DNA–DNA relatedness between strain YMO722T and strain YMO81T was 55 %. N 4-Aminopropylspermine was identified as a major polyamine, which suggested that the isolates were distinct from other related taxa. On the basis of phylogenetic, phenotypic and chemotaxonomic analyses, we propose a new genus, Calditerricola gen. nov., and two novel species, the type species Calditerricola satsumensis sp. nov., with type strain YMO81T (=ATCC BAA-1462T =JCM 14719T =DSM 45223T), and Calditerricola yamamurae sp. nov., with type strain YMO722T (=ATCC BAA-1461T =JCM 14720T =DSM 45224T).

Improvement of film Quality of A-Si:H Deposited by Photo-CVD using SiH2Cl2

Hydrogenated Amorphous silicon films (a-Si:H) were prepared by mercury sensitized photo-CVD using SiH4 and SiH2Cl2 gas mixture. The effects of chlorine (Cl) on the electrical, optical and structural properties of the a-Si:H films were investigated. It was found that a small addition of SiH2Cl2 to the deposition system increases the photo-sensitivity, decreases the defect density, and reduces the light induced degradation of a-Si:H films. At a large addition of SiH2Cl2, however, the CI incorporation into the films was observed, resulting in the deterioration of the film properties. The electrical and optical properties were successfully improved by the H2 dilution when the films were deposited with a large addition of SiH2Cl2.

Randomised clinical trial: efficacy of the addition of a prokinetic, mosapride citrate, to omeprazole in the treatment of patients with non-erosive reflux disease - a double-blind, placebo-controlled study

BACKGROUND

Proton pump inhibitors (PPIs) are less effective in non-erosive reflux disease (NERD) patients than in reflux oesophagitis patients. Whether the addition of prokinetics to PPIs improves NERD patients' symptoms remains unknown.

AIM

To evaluate the efficacy of mosapride in NERD patients when used with PPI.

METHODS

A total of 200 NERD patients were randomised to one of two arms: omeprazole (10 mg once daily) plus mosapride citrate (5 mg three times a day) (treatment arm) and omeprazole plus placebo (placebo arm). The primary endpoint was the rate of responders [visual analogue scale (VAS) was zero or <1 cm] after 4 weeks of treatment. The secondary endpoints were changes in the VAS score and the safety profile.

RESULTS

There was no significant difference between the rates of responders in both arms in intent-to-treat (ITT) and per-protocol (PP) analysis. The change in the VAS score in treatment arm was significantly better than placebo arm in PP analysis (-4.0 ± 0.2 and -3.3 ± 0.2, mean ± S.E.M.) (N.S. in ITT analysis). The rate of adverse events was similar in both groups.

CONCLUSION

The addition of mosapride to omeprazole was not more effective than omeprazole alone.

Identification, chemical synthesis, and biological functions of unusual polyamines produced by extreme thermophiles

Unusual long polyamines such as caldopentamine and caldohexamine, and branched polyamines such as tetrakis(3-aminopropyl)ammonium and N (4)-aminopropylspermidine were often found in cells of extreme thermophiles and hyperthermophiles belonging to both Bacteria and Archaea domains. Some of these unusual polyamines are essential for life at extreme temperatures. In some cases, the unusual polyamines also exist in cells of nonthermophilic organisms and play important physiological roles under normal conditions. Methods for chromatographic analysis, isolation, and chemical syntheses of unusual polyamines as well as experimental methods for measuring their physiological roles are discussed. Especially, many newly improved methods for chemical syntheses are presented in this article.

Enigmas of biosyntheses of unusual polyamines in an extreme thermophile, Thermus thermophilus

Thermus thermophilus, an extreme thermophile belonging to Domain Bacteria, produces unusual polyamines in addition to standard polyamines. To understand mechanisms of changes of polyamine compositions of the thermophile upon change of growth conditions such as environmental temperature, metabolic pathways of polyamine biosyntheses of T. thermophilus have been studied and a new polyamine metabolic pathway was proposed. However, many enigmas remain to be solved in future studies. In this paper, biosyntheses of two non-standard polyamines, thermospermine and sym-homospermidine which are also produced and play important roles in plant cells, of the extreme thermophile are discussed in relation to the biosynthetic reactions in plants.

Docking simulation of polyamines on a kissing-loop RNA dimer

Polyamines, especially branched polyamines such as tetrakis(3-aminopropyl)ammonium (Taa), stabilize the tertiary structure of RNA molecules. In this study, we examined the polyamine binding site of the HIV-1 dimerization initiation site (DIS) in the kissing-loop dimer by the docking simulation. It was found that Taa binds predominantly to the kissing loop interaction site of DIS.

NK-1 receptor is involved in the decreased movement in a rat chronic acid reflux oesophagitis model

BACKGROUND

We previously reported that rats with reflux oesophagitis (RE) show a decrease in voluntary movement, which could be used as a measure of chronic visceral symptoms. However, what mediates these symptoms is still unknown, and pain-related neuropeptides or their receptors in oesophageal mucosa are possibly related to the symptom generation of oesophagitis. In the present study, we investigated the role of NK-1 receptor (NK-1R) as a mediator of oesophagitis symptoms.

METHODS

Chronic RE was surgically induced using rats. The degree or severity of oesophageal symptoms was evaluated by assessing voluntary movement, which was monitored using an infrared sensor system. The NK-1R antagonist, L-732,138, was administered and changes in voluntary movement were assessed. Ten days after surgery, the rats were killed to examine the oesophagus. NK-1R and tachykinin-1 mRNA were detected by real-time RT-PCR. NK-1R protein expression was examined by Western blotting.

KEY RESULTS

Voluntary movement of the oesophagitis model rats was significantly lower than that of the sham-operated rats on day 10. The size of oesophageal mucosal erosion did not correlate with the amount of voluntary movement. The amount of NK-1R protein and mRNA in the oesophageal tissue was significantly higher at both the erosion and non-erosion sites. The amount of tachykinin-1 mRNA in oesophageal tissue at the non-erosion sites was significantly higher in oesophagitis rats. The voluntary movement of oesophagitis rats was significantly increased by the administration of L-732,138.

CONCLUSIONS & INFERENCES

The NK-1R and related neuropeptides are possibly involved in the decrease in voluntary movement of RE.

Transcription profile of Thermus thermophilus CRISPR systems after phage infection

The clustered regularly interspaced short palindromic repeat (CRISPR) systems composed of DNA direct repeats designated as CRISPRs and several CRISPR-associated (cas) genes, which are present in many prokaryotic genomes, make up a host defense system against invading foreign replicons such as phages. In order to investigate the altered expression profiles of the systems after phage infection using a model organism, Thermus thermophilus HB8, which has 12 CRISPR loci, genome-wide transcription profiling of the strain infected with lytic phage PhiYS40 was performed by DNA microarray analysis. Significant alteration of overall mRNA expression gradually increased during infection (i.e., from the eclipse period to the period of host cell lysis). Interestingly, the expression of most cAMP receptor protein (CRP)-regulated genes, including two CRISPR-associated (cas) operons, was most markedly up-regulated, especially around the beginning of host cell lysis, although up-regulation of the crp gene was not observed. The expression of the CRP-regulated genes was less up-regulated in a crp-deficient strain than in the wild type. Thus, it is suggested that cAMP is a signaling molecule that transmits information on phage infection to CRP to up-regulate these genes. On the other hand, the expression of several cas genes and that of CRISPRs were up-regulated independent of CRP, suggesting the involvement of unidentified regulatory factor(s) induced by phage infection. On analysis of the expression profile of the entire genome, we could speculate that upon phage infection, the signal was transmitted to the cells, with host response systems including CRISPR defense systems being activated, while the overall efficiencies of transcription, translation, and metabolism in the cells decreased. These findings will facilitate understanding of the host response mechanism following phage infection.

Gain and loss of an intron in a protein-coding gene in Archaea: the case of an archaeal RNA pseudouridine synthase gene

Background

We previously found the first examples of splicing of archaeal pre-mRNAs for homologs of the eukaryotic CBF5 protein (also known as dyskerin in humans) in Aeropyrum pernix, Sulfolobus solfataricus, S. tokodaii, and S. acidocaldarirus, and also showed that crenarchaeal species in orders Desulfurococcales and Sulfolobales, except for Hyperthermus butylicus, Pyrodictium occultum, Pyrolobus fumarii, and Ignicoccus islandicus, contain the (putative) cbf5 intron. However, the exact timing of the intron insertion was not determined and verification of the putative secondary loss of the intron in some lineages was not performed.

Results

In the present study, we determined approximately two-thirds of the entire coding region of crenarchaeal Cbf5 sequences from 43 species. A phylogenetic analysis of our data and information from the available genome sequences suggested that the (putative) cbf5 intron existed in the common ancestor of the orders Desulfurococcales and Sulfolobales and that probably at least two independent lineages in the order Desulfurococcales lost the (putative) intron.

Conclusion

This finding is the first observation of a lineage-specific loss of a pre-mRNA intron in Archaea. As the insertion or deletion of introns in protein-coding genes in Archaea has not yet been seriously considered, our finding suggests the possible difficulty of accurately and completely predicting protein-coding genes in Archaea.

Usefulness and faults of the sentinel lymph node biopsy using dye technique in distal gastrectomy for gastric cancer

e15509

Background: We apply sentinel node biopsy (SNB) in distal gastrectomy to perform it as safe limited surgery. Limited surgery is a procedure in which the extent of lesion resection and lymph node dissection is reduced. We assessed usefulness and faults of intraoperative diagnosis of lymph node metastasis in this regard. Methods: Surgical procedures: Patent blue (1%) is injected submucosally into 4 to 5 different sites at 1 mL per site around the primary tumor. If blue nodes are found, biopsy and diagnosis of metastasis are performed at this point. Subjects and methods: The study was conducted in 96 gastric cancer patients with a preoperative diagnosis of T1 or mp invasion. Informed consent was obtained from the all patients. There were 65 males and 31 females with a mean age of 64.2 years. Tumor invasion of m, sm, mp, ss, and se was identified in 44, 38, 8, 2, and 4 patients, respectively. All patients underwent open distal gastrectomy (DG) (n=31) or laparoscopy-assisted distal gastrectomy (LADG) (n=65) and Billroth-I reconstruction. Results: The mean number of BNs dissected was 4.5 and 3.7 in DG and LADG cases, respectively. Intraoperative identification and biopsy of BNs could be performed in 34 of 35 DG patients and in 58 of 61 LADG patients. Of the 34 patients in whom BNs were identified, 5 had metastases in BNs confirmed by intraoperative frozen section diagnosis in DG cases. On the other hand, of the 58 LADG patients in whom BNs were identified, 5 had metastases in BNs confirmed by intraoperative frozen section diagnosis in LADG case. False-negative rate was 1.9%. Conclusions: SNB can be performed in LADG as well as in DG. For the case that shows infiltration up to MP, the possibility of lymph node metastasis for other lymph node is considered to be negligible. In obese cases we had some cases of no BNs and false-negative. In consequence, as long as the infiltration is lower than MP, and confirmed that metastasis was not found by blue node biopsy, distal gastrectomy using limited surgery would be thought to be done safely.

No significant financial relationships to disclose.

Overexpression of EphA4 gene and reduced expression of EphB2 gene: Correlation with liver metastasis in colorectal cancer

e15129

The Eph receptors, members of a large family of transmembrane receptor tyrosine kinases, play important roles in a variety of biologic functions. Recent studies have suggested that EphA4 and EphB2 participate in the growth and development of various carcinomas. This study examined the relations of EphA4 and EphB2 gene expression to clinicopathological factors, especially metastasis, in patients with colorectal cancer. We studied surgical specimens of cancer tissue and adjacent normal mucosa obtained from 205 patients with untreated colorectal cancer. The relative expression levels of EphA4 and EphB2 mRNA in the specimens were measured by quantitative real-time, reverse-transcription polymerase chain reaction. The relative expression level of EphA4 mRNA was higher in the presence than in the absence of liver metastasis, whereas the relative expression levels of EphB2 mRNA were similar. Analysis of the relations between clinicopathological features and gene expression showed that high expression of the EphA4 gene and low expression of the EphB2 gene correlated with liver metastasis. There was no correlation between EphA4 and EphB2 gene expression. Our results suggest that over-expression of the EphA4 gene and reduced expression of the EphB2 gene might promote liver metastasis in colorectal cancer. Over-expression of the EphA4 gene and reduced expression of the EphB2 gene may thus be a useful predictor of liver metastasis in patients with colorectal cancer.

No significant financial relationships to disclose.

Experimental oesophagitis in the rat is associated with decreased voluntary movement

Growing interest has arisen regarding the mechanism of dyspeptic symptom generation. However, no evaluation system of these symptoms in animals has been developed. In this study, we examined whether voluntary movement of rats could be a measure to assess visceral symptoms of reflux oesophagitis. A chronic acid reflux oesophagitis model was made using rats, and the size of erosions was measured. Omeprazole was administered to the oesophagitis rats for 10 days. The amount of voluntary movement was measured by an infrared sensor. Intracellular spaces in oesophageal epithelium were also measured using a emission electron microscope. NP-40 soluble and insoluble fractions of claudins were examined by Western blot. Voluntary movement was significantly lower in the oesophagitis model rats than in the sham-operated rats (P < 0.01). Although omeprazole reduced the size of erosions, it did not significantly affect the total amount of voluntary movement (r = -0.033, P = 0.916). Intracellular spaces were significantly dilated in the oesophagitis model rats and claudin-3 showed a significantly lower relative quantity in the NP-40 insoluble fraction. Omeprazole significantly increased voluntary movement of oesophagitis model rats and the relative quantity of claudin-3 in the insoluble fraction (P < 0.05). Dilated intercellular spaces and the lower level of claudin-3 may relate to the voluntary movement of oesophagitis model rats. Decreases in voluntary movement of oesophagitis model rats may reflect visceral symptoms and be able to serve as an index of chronic abdominal symptoms.

Crystallization and preliminary X-ray diffraction studies of the prototypal homologue of mitoNEET (Tth-NEET0026) from the extreme thermophile Thermus thermophilus HB8

MitoNEET (a mammalian mitochondrial outer membrane protein) is a potential pharmacological and clinical target of the insulin-sensitizer pioglitazone. The thermophilic homologue of mitoNEET (TTHA0026) from Thermus thermophilus HB8 has been heterologously overproduced in Escherichia coli and purified as a water-soluble prototypal protein containing the mitoNEET-like [2Fe-2S] cluster. The resultant recombinant protein, named Tth-NEET0026, has been crystallized in its oxidized form by the hanging-drop vapour-diffusion method using 17%(w/v) polyethylene glycol 4000, 8.5%(v/v) 2-propanol, 15%(v/v) glycerol and 0.085 M HEPES-NaOH pH 7.2. The dark reddish crystals diffracted to 1.80 A resolution and belonged to the tetragonal space group P4(3)2(1)2, with unit-cell parameters a = 45.51, c = 84.26 A. The asymmetric unit contains one protein molecule.

A preliminary analysis of microbial and biochemical properties of high-temperature compost

We investigated the microbial community of a high-temperature compost process exhibiting an internal temperature exceeding 90 degrees C. The waste pile was crosscut and samples were collected from the bottom to the top of the refuse pile. PCR-denaturing gradient gel electrophoresis analysis suggested that the microbial community of the high-temperature compost is heterogeneous and differs from one locality to another. Heat-stable collagenases and amylases were extracted directly from the compost pile. Collagenases were located in the upper half of the pile, whereas amylases were detected mainly in the lower parts. Several extremely thermophilic strains were isolated at 80 degrees C; these strains were aerobes. Based on 16S rRNA sequence analysis, the isolates clustered together and represent one or two closely related species. We propose that these thermophilic isolates belong to a novel genus, Caldaterra, gen. nov.