Efficiency of peptide nucleic acid-directed PCR clamping and its application in the investigation of natural diets of the Japanese eel leptocephali

Polymerase chain reaction (PCR)-clamping using blocking primer and DNA-analogs, such as peptide nucleotide acid (PNA), may be used to selectively amplify target DNA for molecular diet analysis. We investigated PCR-clamping efficiency by studying PNA position and mismatch with complementary DNA by designing PNAs at five different positions on the nuclear rDNA internal transcribed spacer 1 of the Japanese eel Anguilla japonica in association with intra-specific nucleotide substitutions. All five PNAs were observed to efficiently inhibit amplification of a fully complementary DNA template. One mismatch between PNA and template DNA inhibited amplification of the template DNA, while two or more mismatches did not. DNA samples extracted from dorsal muscle and intestine of eight wild-caught leptochephalus larvae were subjected to this analysis, followed by cloning, nucleotide sequence analysis, and database homology search. Among 12 sequence types obtained from the intestine sample, six were identified as fungi. No sequence similarities were found in the database for the remaining six types, which were not related to one another. These results, in conjunction with our laboratory observations on larval feeding, suggest that eel leptocephali may not be dependent upon living plankton for their food source.     

Updated perspectives on the cytosolic sulfotransferases (SULTs) and SULT-mediated sulfation

The cytosolic sulfotransferases (SULTs) are Phase II detoxifying enzymes that mediate the sulfate conjugation of numerous xenobiotic molecules. While the research on the SULTs has lagged behind the research on Phase I cytochrome P-450 enzymes and other Phase II conjugating enzymes, it has gained more momentum in recent years. This review aims to summarize information obtained in several fronts of the research on the SULTs, including the range of the SULTs in different life forms, concerted actions of the SULTs and other Phase II enzymes, insights into the structure–function relationships of the SULTs, regulation of SULT expression and activity, developmental expression of SULTs, as well as the use of a zebrafish model for studying the developmental pharmacology/toxicology.     

Similar fish species composition despite larger environmental heterogeneity during severe hypoxia in a coastal ecosystem

Environmental heterogeneity is one of the most influential factors that create compositional variation among local communities. Greater compositional variation is expected when an environmental gradient encompasses the most severe conditions where species sorting is more likely to operate. However, evidence for stronger species sorting at severer environment has typically been obtained for less mobile organisms and tests are scarce for those with higher dispersal ability that allows individuals to sensitively respond to environmental stress. Here, with the dynamics of fish communities in a Japanese bay revealed by environmental DNA metabarcoding analyses as a model case, we tested the hypothesis that larger environmental heterogeneity caused by severe seasonal hypoxia (lower concentration of oxygen in bottom waters in summer) leads to larger variation of species composition among communities. During summer, fish species richness was lower in the bottom layer, suggesting the severity of the hypoxic bottom water. In contrast to the prediction, we found that although the environmental parameters of bottom and surface water was clearly distinct in summer, fish species composition was more similar between the two layers. Our null model analysis suggested that the higher compositional similarity during hypoxia season was not a result of the sampling effect reflecting differences in the alpha or gamma diversity. Furthermore, a shift in the species occurrence from bottom to surface layers was observed during hypoxia season, which was consistent across species, suggesting that the severe condition in the bottom adversely affected fish species irrespective of their identity. These results suggest that larger environmental heterogeneity does not necessarily lead to higher compositional variation once the environmental gradient encompasses extremely severe conditions. This is most likely because individual organisms actively avoided the severity quasi‐neutrally, which induced mass effect‐like dispersal and lead to the mixing of species composition across habitats. By showing counter evidence against the prevailing view, we provide novel insights into how species sorting by environment acts in heterogeneous and severe conditions.     

Green tea polyphenol epigallocatechin gallate activates TRPA1 in an intestinal enteroendocrine cell line, STC-1

A characteristic astringent taste is elicited by polyphenols. Among the polyphenols, catechins and their polymers are the most abundant polyphenols in wine and tea. A typical green tea polyphenol is epigallocatechin gallate (EGCG). Currently, the mechanism underlying the sensation of astringent taste is not well understood. We observed by calcium imaging that the mouse intestinal endocrine cell line STC-1 responds to the astringent compound, EGCG. Among major catechins of green tea, EGCG was most effective at eliciting a response in this cell line. This cellular response was not observed in HEK293T or 3T3 cells. Further analyses demonstrated that the 67-kDa laminin receptor, a known EGCG receptor, is not directly involved. The Ca(2+) response to EGCG in STC-1 cells was decreased by inhibitors of the transient receptor potential A1 (TRPA1) channel. HEK293T cells transfected with the mouse TRPA1 (mTRPA1) cDNA showed a Ca(2+) response upon application of EGCG, and their response properties were similar to those observed in STC-1 cells. These results indicate that an astringent compound, EGCG, activates the mTRPA1 in intestinal STC-1 cells. TRPA1 might play an important role in the astringency taste on the tongue.     

Strobilomyces mirandus Corner, a new record from Japan

Strobilomyces mirandus, a bolete new to Japan, is described and illustrated. This is the first record of the species outside of the type locality in Malaysia. It is very distinct from other Strobilomyces species by the unusually colored yellow or golden-orange to brownish-orange of the basidiocarp.     

Crystal structure of mSULT1D1, a mouse catecholamine sulfotransferase

In mammals, sulfonation as mediated by specific cytosolic sulfotransferases (SULTs) plays an important role in the homeostasis of dopamine and other catecholamines. To gain insight into the structural basis for dopamine recognition/binding, we determined the crystal structure of a mouse dopamine-sulfating SULT, mouse SULT1D1 (mSULT1D1). Data obtained indicated that mSULT1D1 comprises of a single α/β domain with a five-stranded parallel β-sheet. In contrast to the structure of the human SULT1A3 (hSULT1A3)-dopamine complex previously reported, molecular modeling and mutational analysis revealed that a water molecule plays a critical role in the recognition of the amine group of dopamine by mSULT1D1. These results imply differences in substrate binding between dopamine-sulfating SULTs from different species.     

Effect of Polyphenols on the Growth and Enzymes of Some Animal Cells

The effect was investigated of some polyphenol compounds on the growth and intracellular enzyme activity of human-derived cells and Chinese hamster ovary (CHO) cells. Quercetin, a mutagen, inhibited the growth of serum-free cultured human-human hybridomas (SI102 and HB4C5) and a human histiocytic lymphoma cell line (U-937), but did not affect the growth of CHO cells. Glycosides of quercetin such as quercetin-4′-glucoside (Q-4′-G), quercetin-3,4′-glucoside (Q-3,4′-G) and rutin, and other polyphenol compounds (catechin and epicatechin) had no significant inhibiting effect on the growth of human-derived cells or CHO cells. These compounds slightly promoted the growth of human-derived cells. Most of the polyphenols used increased the activity of a drug-metabolizing enzyme, NADPH-cytochrome C reductase, in the U-937 cells and CHO cells, this effect being more marked in the CHO cells than in the U-937 cells. Quercetin markedly reduced the activity of catalase in the human-derived cell lines, while it slightly activated catalase in the CHO cells. Rutin, Q-4′-G, Q-3,4′-G, catechin and epicatechin produced no significant change in catalase activity. Quercetin also reduced the activity of glutamic oxaloacetic transaminase in the U-937 cells.     

Light-Sensitive Vertical Migration of the Japanese Eel Anguilla japonica Revealed by Real-Time Tracking and Its Utilization for Geolocation

Short-time tracking (one to eight days) of the Japanese eel (Anguilla japonica) using ultrasonic transmitter was performed in the tropical-subtropical area adjacent to the spawning area and temperate area off the Japanese Archipelago. Of 16 eels (11 wild and five farmed) used, 10 wild eels displayed clear diel vertical migration (DVM) from the beginning, while the other five farmed eels tracked for 19 to 66 hours did not. During daytime, a significantly positive correlation between migration depth and light intensity recorded on the vessel was observed in the 10 wild eels, indicating that the eels were sensitive to sunlight even at the middle to lower mesopelagic zone (500 to 800 m). During nighttime, the eel migration depth was observed to be associated with the phase, rising and setting of the moon, indicating that the eels were sensitive to moonlight at the upper mesopelagic zone (<300 m). Two of 10 wild eels were in the yellow stage but shared similar DVM with the silver stage eels. Swimbladders of three silver stage eels were punctured before releasing, but very little effect on DVM was observed. The eels very punctually initiated descent upon nautical dawn and ascent upon sunset, enabling us to determine local times for sunrise and sunset, and hence this behavior may be used for geolocating eels. In fact, estimated positions of eels based on the depth trajectory data were comparable or even better than those obtained by light-based archival tag in other fish species.     

Novel Mode of Cooperative Binding between Myosin and Mg-actin Filaments in the Presence of Low Concentrations of ATP

Cooperative interaction between myosin and actin filaments has been detected by a number of different methods, and has been suggested to have some role in force generation by the actomyosin motor. In this study, we observed the binding of myosin to actin filaments directly using fluorescence microscopy to analyze the mechanism of the cooperative interaction in more detail. For this purpose, we prepared fluorescently labeled heavy meromyosin (HMM) of rabbit skeletal muscle myosin and Dictyostelium myosin II. Both types of HMMs formed fluorescent clusters along actin filaments when added at substoichiometric amounts. Quantitative analysis of the fluorescence intensity of the HMM clusters revealed that there are two distinct types of cooperative binding. The stronger form was observed along Ca²⁺-actin filaments with substoichiometric amounts of bound phalloidin, in which the density of HMM molecules in the clusters was comparable to full decoration. The novel, weaker form was observed along Mg²⁺-actin filaments with and without stoichiometric amounts of phalloidin. HMM density in the clusters of the weaker form was several-fold lower than full decoration. The weak cooperative binding required sub-micromolar ATP, and did not occur in the absence of nucleotides or in the presence of ADP and ADP-Vi. The G680V mutant of Dictyostelium HMM, which over-occupies the ADP-Pi bound state in the presence of actin filaments and ATP, also formed clusters along Mg²⁺-actin filaments, suggesting that the weak cooperative binding of HMM to actin filaments occurs or initiates at an intermediate state of the actomyosin-ADP-Pi complex other than that attained by adding ADP-Vi.