Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing

For the analysis of microbial community structure based on 16S rDNA sequence diversity, sensitive and robust PCR amplification of 16S rDNA is a critical step. To obtain accurate microbial composition data, PCR amplification must be free of bias; however, amplifying all 16S rDNA species with equal efficiency from a sample containing a large variety of microorganisms remains challenging. Here, we designed a universal primer based on the V3-V4 hypervariable region of prokaryotic 16S rDNA for the simultaneous detection of Bacteria and Archaea in fecal samples from crossbred pigs (Landrace×Large white×Duroc) using an Illumina MiSeq next-generation sequencer. In-silico analysis showed that the newly designed universal prokaryotic primers matched approximately 98.0% of Bacteria and 94.6% of Archaea rRNA gene sequences in the Ribosomal Database Project database. For each sequencing reaction performed with the prokaryotic universal primer, an average of 69,330 (±20,482) reads were obtained, of which archaeal rRNA genes comprised approximately 1.2% to 3.2% of all prokaryotic reads. In addition, the detection frequency of Bacteria belonging to the phylum Verrucomicrobia, including members of the classes Verrucomicrobiae and Opitutae, was higher in the NGS analysis using the prokaryotic universal primer than that performed with the bacterial universal primer. Importantly, this new prokaryotic universal primer set had markedly lower bias than that of most previously designed universal primers. Our findings demonstrate that the prokaryotic universal primer set designed in the present study will permit the simultaneous detection of Bacteria and Archaea, and will therefore allow for a more comprehensive understanding of microbial community structures in environmental samples.     

Deletion analysis of the superoxide dismutase (sodM) promoter from Aspergillus oryzae

The manganese superoxide dismutase gene (sodM) is very highly expressed in Aspergillus oryzae. To elucidate the basis for this high-level expression, deletion analysis of the promoter was undertaken using β-glucuronidase (GUS) as a reporter. Deletion of a 63-bp sequence from −200 to −138 in the 1,038-bp sodM promoter caused a drastic decrease in GUS activity. In addition, an electrophoretic gel mobility shift assay (EMSA) implicated a 30-bp element from −209 to −178 containing cis-element(s) in the high-level expression. The results of fine structure deletion analysis of this region were consistent with the EMSA results. To confirm these findings, we constructed enhanced sodM promoters by incorporating tandem repeats of this region, which resulted in an approximate twofold increase in expression relative to the native sodM promoter.     

Anoplin, a novel antimicrobial peptide from the venom of the solitary wasp Anoplius samariensis.

A novel antimicrobial peptide, anoplin, was purified from the venom of the solitary wasp Anoplius samariensis. The sequence was mostly analyzed by mass spectrometry, which was corroborated by solid-phase synthesis. Anoplin, composed of 10 amino acid residues, Gly-Leu-Leu-Lys-Arg-Ile-Lys-Thr-Leu-Leu-NH2, has a high homology to crabrolin and mastoparan-X, the mast cell degranulating peptides from social wasp venoms, and, therefore, can be predicted to adopt an amphipathic alpha-helix secondary structure. In fact, the circular dichroism (CD) spectra of anoplin in the presence of trifluoroethanol or sodium dodecyl sulfate showed a high content, up to 55%, of the alpha-helical conformation. A modeling study of anoplin based on its homology to mastoparan-X supported the CD results. Biological evaluation using the synthetic peptide revealed that this peptide exhibited potent activity in stimulating degranulation from rat peritoneal mast cells and broad-spectrum antimicrobial activity against both Gram-positive and Gram-negative bacteria. Therefore, this is the first antimicrobial component to be found in the solitary wasp venom and it may play a key role in preventing potential infection by microorganisms during prey consumption by their larvae. Moreover, this peptide is the smallest among the linear alpha-helical antimicrobial peptides hitherto found in nature, which is advantageous for chemical manipulation and medical application.     

Transmural and apicobasal gradients in repolarization contribute to T-wave genesis in human surface ECG

The cellular basis of the T-wave morphology of surface ECG remains controversial in clinical cardiology. We examined the effect of action potential duration (APD) distribution on T-wave morphology using a realistic model of the human ventricle and torso. We developed a finite-element model of the ventricle consisting of ～26 million elements, including the conduction system, each implemented with the ion current model of cardiomyocytes. This model was embedded in a torso model with distinct organ structures to obtain the standard ECG leads. The APD distribution was changed in the transmural direction by locating the M cells in either the endocardial or epicardial region. We also introduced apicobasal gradients by modifying the ion channel parameters. Both the transmural gradient (with M cells on the endocardial side) and the apicobasal gradient produced positive T waves, although a very large gradient was required for the apicobasal gradient. By contrast, T waves obtained with the transmural gradient were highly symmetric and, therefore, did not represent the true physiological state. Only combination of the transmural and the moderate apicobasal gradients produced physiological T waves in surface ECG. Positive T waves in surface ECG mainly originated from the transmural distribution of APD with M cells on the endocardial side, although the apicobasal gradient was also required to attain the physiological waveform.     

Distribution pattern of anthocyanins in the polygonaceae

A survey of anthocyanins in the flowers and other organs of thirty-three species of three genera belonging to the Polygonaceae has been carried out. There are thirteen anthocyans. Cyanidin glycosides, especially the 3-glycoside (chrysanthemin), are present most commonly and peonidin glycosides including the arabinosylglucoside are found with low frequency. The distribution of malvidin 3,5-diglucoside (malvin) is confined to the species belonging to the sectionEchinocaulon of the genusPolygonum. It is noted that cyanidin itself occurs in the stems ofPolygonum perfoliatum andP. senticosum.     

Behavioral and other systemic effects of cortisol-21 sulfate

Three milligrams of cortisol-21 -sulfate or cortisol free alcohol in oil suspension was administered intramuscularly to male rats on alternate days for 2–7 weeks. Open-field tests repeated at 2- or 3-day intervals revealed that both steroids had significant stimulatory effects on the animal's exploratory behaviors (ambulation and rearing), when the treatments were started soon after weaning (postnatal day 21–24). The same treatments to adult rats (46 days old), however, did not cause any change in the activity levels. It was also shown that cortisol sulfate, in contrast to free cortisol, was inert as a glucocorticoid; it had no catabolic, gluconeogenic, lympholytic, or ACTH-suppressive effects. The results suggest that cortisol sulfate, and probably free cortisol as well, affects behavior through its direct action on the central nervous system rather than via its effects on intermediary metabolism or negative feedback on pituitary ACTH release.     

Phenolic compounds from Forsythia leaves

Four lignans, four lignan glucosides, one flavonoid and two caffeoyl glycosides of 3,4-dihydroxyphenethyl alcohol were identified variously in leaves of Forsythia suspensa, F. viridissima and F. koreana. The leaf patterns were broadly similar to those reported earlier for the fruits, except that suspensaside and β-hydroxyacteoside were not detected.     

Sustained release of hCG minipellet for newt experiment in space.

Sustained release formulation of hCG, hCG minipellet, was applied to induce oviposition of newt. Period of egg spawning was prolonged with a certain delay of its initiation. When hCG minipellet was injected to newt that was hibernating, it induced egg spawning even after one month of hibernation. Results suggest that minipellet keeps steady concentration of hCG at the effective level for longer period. For the study on early development of newt egg, it is essential to obtain egg on orbit. hCG minipellet makes it possible even at launch slip or early "late access".