Crystal structure of Nanoarchaeum equitans tyrosyl-tRNA synthetase and its aminoacylation activity toward tRNATyr with an extra guanosine residue at the 5'-terminus

tRNA^Tyr of Nanoarchaeum equitans has a remarkable feature with an extra guanosine residue at the 5'-terminus. However, the N. equitans tRNA^Tyr mutant without extra guanosine at the 5'-end was tyrosylated by tyrosyl-tRNA synthase (TyrRS). We solved the crystal structure of N. equitans TyrRS at 2.80 Å resolution. By comparing the present solved structure with the complex structures TyrRS with tRNA^Tyr of Thermus thermophilus and Methanocaldococcus jannaschii, an arginine substitution mutant of N. equitans TyrRS at Ile200 (I200R), which is the putative closest candidate to the 5'-phosphate of C1 of N. equitans tRNA^Tyr, was prepared. The I200R mutant tyrosylated not only wild-type tRNA^Tyr but also the tRNA without the G-1 residue. Further tyrosylation analysis revealed that the second base of the anticodon (U35), discriminator base (A73), and C1:G72 base pair are strong recognition sites.

Correction to: G:U‑Independent RNA Minihelix Aminoacylation by Nanoarchaeum equitans Alanyl‑tRNA Synthetase: An Insight into the Evolution of Aminoacyl‑tRNA Synthetases

In the original version of this article, "A73" in Fig 6b was inadvertently labeled as "G73". The corrected Fig. 6 is given here.

Anisotropic Fully Gapped Superconductivity Possibly Mediated by Charge Fluctuations in a Nondimeric Organic Complex

We investigate low-temperature electronic properties of the nondimeric organic superconductor β^{''}-(ET)_{4}[(H_{3}O)Ga(C_{2}O_{4})_{3}]PhNO_{2}. By examining ultrasonic properties, charge disproportionation (CD) without magnetic field dependence is detected below T_{CD}∼8  K just above the superconducting critical temperature T_{c}∼6  K. From quantum oscillations in high fields, we find variation in the Fermi surface and mass enhancement induced by the CD. Heat capacity studies elucidate that the superconducting gap function is fully gapped in the Fermi surface, but anisotropic with fourfold symmetry. We point out that the pairing mechanism of the superconductivity is possibly dominated by charge fluctuations.

Aminoacylation of short hairpin RNAs through kissing-loop interactions indicates evolutionary trend of RNA molecules

The unique G3:U70 base pair in the acceptor stem of tRNA^Ala has been shown to be a critical recognition site by alanyl-tRNA synthetase (AlaRS). The base pair resides on one of the arms of the L-shaped structure of tRNA (minihelix) and the genetic code has likely evolved from a primordial tRNA-aaRS (aminoacyl-tRNA synthetase) system. In terms of the evolution of tRNA, incorporation of a G:U base pair in the structure would be important. Here, we found that two independent short hairpin RNAs change their conformation through kissing-loop interactions, finally forming a minihelix-like structure, in which the G3:U70 base pair is incorporated. The RNA system can be properly aminoacylated by the minimal Escherichia coli AlaRS variant with alanylation activity (AlaRS442N). Thus, characteristic structural features produced via kissing-loop interactions may provide important clues into the evolution of RNA.

Diagonal nematicity in the pseudogap phase of HgBa2CuO4+δ

The pseudogap phenomenon in the cuprates is arguably the most mysterious puzzle in the field of high-temperature superconductivity. The tetragonal cuprate HgBa₂CuO_4+δ, with only one CuO₂ layer per primitive cell, is an ideal system to tackle this puzzle. Here, we measure the magnetic susceptibility anisotropy within the CuO₂ plane with exceptionally high-precision magnetic torque experiments. Our key finding is that a distinct two-fold in-plane anisotropy sets in below the pseudogap temperature T^*, which provides thermodynamic evidence for a nematic phase transition with broken four-fold symmetry. Surprisingly, the nematic director orients along the diagonal direction of the CuO₂ square lattice, in sharp contrast to the bond nematicity along the Cu-O-Cu direction. Another remarkable feature is that the enhancement of the diagonal nematicity with decreasing temperature is suppressed around the temperature at which short-range charge-density-wave formation occurs. Our result suggests a competing relationship between diagonal nematic and charge-density-wave order in HgBa₂CuO_4+δ.

Comparison of the Airway Scope®, gum elastic bougie and fibreoptic bronchoscope in simulated difficult tracheal intubation: a manikin study

We compared the Airway Scope with a gum elastic bougie and fibreoptic bronchoscope in a manikin with a simulated Cormack and Lehane Grade 3 laryngoscopic view. Twenty-seven anaesthetists intubated the trachea of the manikin with these devices and the time required for intubation was measured. They were then asked to rate the subjective difficulty of intubation (1 = very easy; 5 = very difficult). Mean (SD) intubation times were 16.6 (11.2) s with the Airway Scope, 29.4 (10.9) s with the gum elastic bougie (p < 0.0001), and 30.6 (20.0) s with the fibreoptic bronchoscope (p < 0.0001). The median (range) difficulty was 2 (1-4) with the Airway Scope, 3 (2-4) with the gum elastic bougie (p < 0.001), and 2 (1-5) with the fibreoptic bronchoscope (p = 0.014). In Cormack and Lehane grade 3 laryngoscopic views, the Airway Scope may enable faster and easier tracheal intubation than does a Macintosh laryngoscope with a gum elastic bougie or a fibreoptic bronchoscope.

Estrogenic activity in sediments contaminated by nonylphenol in Tokyo Bay (Japan) evaluated by vitellogenin induction in male mummichogs (Fundulus heteroclitus)

Estrogenic activity was determined in sediments collected from Tokyo Bay. Sampling was performed at five stations including the site near the sewage treatment plant. The most estrogenic sediment collected near the sewage treatment plant was fractionated into ten fractions using normal-phase high-performance liquid chromatography. Chemical analysis was carried out for each fraction and nonylphenol (NP, 20,700ngg(-1)drywt) was detected at a higher concentration than estron (2.39ngg(-1)drywt) and 17beta-estradiol (<0.7ng g(-1)dry wt). Furthermore, each fraction was administered to male mummichogs (Fundulus heteroclitus), and vitellogenin (Vtg) was measured after two weeks. The induction of Vtg was observed; this estrogenic potency could be attributed to the NP content in this fraction. This is the first report to suggest that the high NP concentration in the sediments from Tokyo Bay has the potential to induce Vtg in wild fish.

Randomized placebo-controlled trial assessing the effect of bifidobacteria-fermented milk on active ulcerative colitis

BACKGROUND

Probiotics are efficacious for treating and maintaining remission of ulcerative colitis.

AIM

To conduct a randomized placebo-controlled trial of bifidobacteria-fermented milk supplementation as a dietary adjunct in treating active ulcerative colitis.

METHODS

Twenty patients with mild to moderate, active, ulcerative colitis randomly received 100 mL/day of bifidobacteria-fermented milk or placebo for 12 weeks with conventional treatment.

RESULTS

Clinical and endoscopic activity indices and histological scores were similar in the two groups before treatment. Although improvements were significant in both groups, the clinical activity index was significantly lower in the bifidobacteria-fermented milk than in the placebo group after treatment. The post-treatment endoscopic activity index and histological score were significantly reduced in the bifidobacteria-fermented milk, but not the placebo group. Increases in faecal butyrate, propionate and short-chain fatty acid concentrations were significant in the bifidobacteria-fermented milk, but not the placebo group. No adverse effects were observed in either group.

CONCLUSION

Supplementation with this bifidobacteria-fermented milk product is safe and more effective than conventional treatment alone, suggesting possible beneficial effects in managing active ulcerative colitis. This is a pilot study and further larger studies are required to confirm the result these preliminary results.

Analysis of SIDS-related civil and criminal court cases in Japan

Thirty-three sudden infant death syndrome (SIDS)-related civil and criminal lawsuits in Japan were retrieved from judicial precedent databases "Hanrei Masutar (Judicial Decisions Master)" and "Hanrei Taikei (Judicial Decisions System) using "SIDS" as a keyword. Sleeping posture and developmental stage of occurrence were studied in each of the cases retrieved, whether or not a legal autopsy had been performed. The influence exerted on court decisions by Japanese definitions of SIDS as well as the relationship between causes of death and court decisions were studied. Of 33, two were criminal cases (business/professional negligence on the part of the defendants, leading to death), and the rest were civil cases (claims for damages). Because the decision handed down in both criminal cases was "cause of death unknown", these defendants were found innocent. One of these cases was argued in both the court of appeals and the superior court: these courts found SIDS to be the cause of death and consequently the claim for damages was rejected. Both criminal and civil courts dealt with another case: the former found the cause of death to be "unknown" and the defendant innocent, while the latter, finding SIDS the cause of death, declined to review. In cases where the sleeping posture was prone, courts tended to decide the cause of death to be suffocation, especially with neonates. Because diagnosis by exclusion is required in cases of a legal autopsy for SIDS, the diagnosis is difficult without an autopsy. Disagreements between the results of legal autopsy and court decisions occurred in eight cases. With such a discrepancy, a detailed case examination is necessary. In 1983, SIDS was defined in Japan in two different ways; one in a more strict sense and the other being more inclusive. The wider and narrower definitions were unified in 1995 by requiring a survey of the circumstances of death in addition to the narrower definition. Because of this situation, the two cases in the 1980s when legal autopsy was not enforced fell into the category of "SIDS in a wider sense." In no case was a defendant found guilty when the cause of death was judged to be either SIDS/ALTE or unknown. Four cases were rejected when the cause of death was judged to be neither due to suffocation nor SIDS, while seven were accepted either as cases of "joint faults that canceled each other," or as "partial acceptance." In Japan, official views concerning a SIDS diagnosis differ among pediatricians, legal scholars of forensic medicine and pathologists. These differences appeared to influence the legal decisions. Several conferences should be convened as soon as possible to provide an opportunity to resolve the main points of difference between these three professional groups and, thus, attain a unified view.

Sensitive determination of four general anaesthetics in human whole blood by capillary gas chromatography with cryogenic oven trapping

Four general anaesthetics, sevoflurane, isoflurane, enflurane and halothane, in human whole blood, have been found measurable with very high sensitivity by capillary gas chromatography-flame ionization detection (GC-FID) with cryogenic oven trapping upon injection of headspace (HS) vapor sample. To a 7-ml vial, containing 0.48 ml of distilled water and 20 microl of internal standard solution (5 microg), a 0.5-ml of whole blood sample spiked with or without anaesthetics, was added, and the mixture was heated at 55 degrees C for 15 min. A measure of 10 ml HS vapor was injected into the GC in the splitless mode at -40 degrees C oven temperature, which was programmed up to 250 degrees C. All four peaks were clearly separated; no impurity peaks were found among their peaks. Their extraction efficiencies were about 10%. The calibration curves showed good linearity in the range of 0.5-20 microg/ml; their detection limits were 10-100 ng/ml, which are almost comparable to those by previous reports. The coefficients of intra-day and day-to-day variations were 6.5-9.8 and 7.3-17.2%, respectively. Isoflurane or enflurane was also measured from whole blood samples in which three volunteers inhaled each compound.

Sensitive determination of midazolam and identification of its two metabolites in human body fluids by column-switching capillary high-performance liquid chromatography/fast atom bombardment-mass spectrometry

Midazolam is a benzodiazepine and is widely prescribed for preanesthesia or general anesthesia. Overdose or intoxication cases of midazolam have been reported. In Japan, smuggled midazolam tablets could be involved in some criminal cases. Midazolam and its two metabolites were extracted by the solid-phase extraction method using Bond Elut SCX cartridges. The compounds were analyzed by on-line capillary high-performance liquid chromatography/fast atom bombardment-mass spectrometry. Midazolam and its two metabolites were well separated on the chromatogram, and each mass spectra gave [M+H](+) ion as a base peak. Deuterium-labeled midazolam was synthesized as an internal standard; it has enabled precise and reproducible quantitation of midazolam in blood samples. The calibration curve showed excellent linearity in the range of 2-200 ng/ml in spiked serum. The detection limit was 300 pg/ml (signal-to-noise ratio=3). The whole blood and urine samples from the victim of a homicide case were analyzed, and the midazolam concentration in the whole blood was estimated to be 163 ng/ml. The present method should be useful in clinical and forensic toxicology, because of its high sensitivity and specificity.

Sensitive determination of pethidine in body fluids by surface ionization organic mass spectrometry

We have presented a simple and sensitive method for determining pethidine, a narcotic analgesic drug in body fluids by gas chromatography (GC)/surface ionization organic mass spectrometry (SIOMS). Good linearity was obtained in the range of 0.625-25 ng/ml of whole blood and urine by mass chromatography, and in the range of 0.05-2 ng/ml of whole blood by selected ion monitoring (SIM). Pethidine and diphenylpyraline (internal standard) were extracted from body fluids with Bond Elut Certify cartridges; their recoveries were above 95%. The detection limits (signal-to-noise ratio=3) were estimated to be 0.2 ng/ml of whole blood or urine by mass chromatography, 0.02 ng/ml of whole blood by SIM.

Sensitive determination of mianserin and setiptiline in body fluids by gas chromatography with surface ionization detection (GC-SID)

Tetracyclic antidepressants, mianserin and setiptiline, in human body fluids have been found measurable with high sensitivity by gas chromatography (GC) with surface ionization detection (SID). The compounds in human whole blood or urine samples were extracted by solid-phase extraction using Bond Elut C(18) cartridges. The recoveries of both compounds from the body fluids were above 85%. For quantitation of mianserin, 25 ng of setiptiline was used as internal standard; and for quantitation of setiptiline, vice versa. The calibration curves for spiked whole blood or urine samples were linear in the range of 1.25-50 ng/ml. The detection limit of mianserin and setiptiline was about 1 ng/ml, which is comparable to those obtained by the previous GC-mass spectrometry methods. Our method seems very useful for determination of mianserin and setiptiline in forensic and clinical toxicology, because of high sensitivity, low background impurities and easy handling of the GC instrument.

Effect of enhanced proteolysis on formation of biogenic amines by lactobacilli during Gouda cheese ripening

The effect of enhanced proteolysis on amine formation by amino acid decarboxylase positive Lactobacillus sp. during Gouda cheese ripening was examined. A commercial proteolytic enzyme preparation was added to pasteurized milk prior to cheese preparation. The effect of this manipulation on the formation of putrescine, histamine and tyramine was investigated in the presence and absence of amino acid decarboxylase-positive strains during a 12-week ripening period. Four batches were supplemented with a proteolytic enzyme. Batch I contained the proteolytic enzyme only, whereas batches II-IV were additionally supplemented with Lactobacillus delbrueckii LTH 1260 (batch II), Lactobacillus buchneri LTH 1388 (batch III) or Lactobacillus brevis LTH 2560 (batch IV). In batch I putrescine was detected with 4 mg/kg, in batch II, 42 mg/kg putrescine, 238 mg/kg histamine and 636 mg/kg tyramine were found. Batch III contained 13 mg/kg putrescine and 418 mg/kg histamine, whereas in batch IV, 26 mg/kg putrescine and 776 mg/kg tyramine were present. Batch V was supplemented with all three lactobacilli but did not contain the proteolytic enzyme. In this experiment, 4 mg/kg putrescine, 179 mg/kg histamine and 337 mg/kg tyramine were detected. A control cheese batch (VI) without addition of amine forming lactobacilli or a proteolytic enzyme was produced and only 4 mg/kg putrescine were detected. An increase in amine concentration during cheese ripening under conditions of enhanced proteolysis in the presence of starter and spoilage lactobacilli was evident from the experiments.

Effect of recombinant human colony-stimulating factor on the course of parasitaemia in non-lethal rodent malaria

The effect of repeated subcutaneous injections of recombinant human granulocyte colony-stimulating factor (rhG-CSF) on the attenuated Plasmodium berghei XAT infection in CBA mice was examined. When mice were injected with rhG-CSF daily beginning 2 days before infection, the neutrophil count in the peripheral blood increased 5 times higher than that of control mice and the development of parasitaemia was suppressed significantly during the early phase of the infection. This suppressive effect of rhG-CSF was reduced by treatment of the mice with either anti-interferon (IFN)-gamma or anti-tumour necrosis factor (TNF)-alpha immunoglobulins. These results suggest that neutrophils may have a role in immunity against the parasites and that IFN-gamma and TNF-alpha are possibly involved.