Rapid degradation of longer DNA fragments enables the improved estimation of distribution and biomass using environmental DNA

The advent of environmental DNA (eDNA) analysis methods has enabled rapid and wide‐range ecological monitoring in aquatic ecosystems, but there is a dearth of information on eDNA degradation. The results of previous studies suggest that the decay rate of eDNA varies depending on the length of DNA fragments. To examine this hypothesis, we compared temporal change in copy number of long eDNA fragments (719 bp) with that of short eDNA fragments (127 bp). First, we isolated rearing water from a target fish species, Japanese Jack Mackerel (Trachurus japonicus), and then quantified the copy number of the long and short eDNA fragments in 1 L water samples after isolating the water from the fish. Long DNA fragments showed a higher decay rate than short fragments. Next, we measured the eDNA copy numbers of long and short DNA fragments using field samples, and compared them with fish biomass as measured by echo intensity. Although a previous study suggested that short eDNA fragments could be overestimated because of nontarget eDNA from a nearby fish market and carcasses, the eDNA concentrations of long fragments were correlated with echo intensity. This suggests that the concentration of longer eDNA fragments reflects fish biomass more accurately than the previous study by removing the effects of the fish market and carcasses. The length‐related differences in eDNA have a substantial potential to improve estimation of species biomass.     

Free nitrous acid and pH determine the predominant ammonia-oxidizing bacteria and amount of N2O in a partial nitrifying reactor

Applied Microbiology and Biotechnology - We investigated the effects of free ammonia (FA) and free nitrous acid (FNA) concentrations on the predominant ammonia-oxidizing bacteria (AOB) and the...     

Genetic dissection of grain traits in Yamadanishiki,an excellent sake-brewing rice cultivar

Key message

The grain traits of Yamadanishiki, an excellent sake-brewing rice cultivar in Japan, are governed by multiple QTLs, namely, a total of 42 QTLs including six major QTLs.

Abstract

Japanese rice wine (sake) is produced using brewing rice (Oryza sativa L.) that carries traits desirable for sake-brewing, such as a larger grain size and higher white-core expression rate (WCE) compared to cooking rice cultivars. However, the genetic basis for these traits in brewing rice cultivars is still unclear. We performed analyses of quantitative trait locus (QTL) of grain and days to heading over 3 years on populations derived from crosses between Koshihikari, a cooking rice, and Yamadanishiki, an excellent sake-brewing rice. A total of 42 QTLs were detected for the grain traits, and the Yamadanishiki alleles at 16 QTLs contributed to larger grain size. Two major QTLs essential for regulating both 100-grain weight (GWt) and grain width (GWh) were harbored in the same regions on chromosomes 5 and 10. An interaction was noted between the environment and the QTL associated with WCE on chromosome 6, which was detected in two of 3 years. In addition, two QTLs for WCE on chromosomes 3 and 10 overlapped with the QTLs for GWt and GWh, suggesting that QTLs associated with grain size also play an important role in the formation of white-core. Despite differences in the rate of grain growth in both Koshihikari and Yamadanishiki across 2 years, the WCE in Yamadanishiki remained consistent, thus demonstrating that the formation of white-core does not depend on grain filling speed. These data can be informative for programs involved in breeding better cooking and brewing rice cultivars.

     

Impairment of the stress response in matrinxã juveniles (Brycon amazonicus) exposed to low concentrations of phenol

In this study we measured plasma cortisol, plasma glucose, plasma sodium and potassium, and liver and gill hsp70 levels in juvenile matrinxã (Brycon amazonicus) subjected to a 96 h exposure to phenol (0, 0.2, and 2.0 ppm), and the effect of this exposure on their ability to respond to a subsequent handling stress. Fish were sampled prior to initiation of exposure and 96 h, and at 1, 6, 12, and 24 h post-handling stress. During the 96 h exposure, plasma cortisol and glucose levels remained unchanged in all treatments. While plasma sodium levels were significantly reduced in all groups, plasma potassium levels only decreased in fish exposed to 0 and 0.2 ppm of phenol. Liver hsp70 levels decreased significantly at 96 h in fish exposed to 2.0 ppm of phenol. All groups, except fish exposed to 0.2 ppm of phenol, were able to increase plasma cortisol and glucose levels after handling stress. Fish exposed to 2.0 ppm of phenol showed decreased gill and liver hsp70 levels after the handling stress. Our data suggest that exposure to phenol may compromise the ability of matrinxã to elicit physiological responses to a subsequent stressor.     

The effects of the preference for music on sleep inertia after a short daytime nap

Sleep and Biological Rhythms - The effects of the preference for excitative music on sleep inertia after a daytime nap were examined. Sixteen young healthy adults took a 20-min nap at 14:00 after...     

Auditory event-related potentials from a single-stimulus paradigm during rapid eye movement sleep

Sleep and Biological Rhythms - Auditory evoked potentials to a 2000-Hz pure tone were recorded in wakefulness and in rapid eye movement (REM) sleep. A late positive wave with a maximal amplitude...     

Protective effects of Choto-san and hooks and stems of Uncaria sinensis against delayed neuronal death after transient forebrain ischemia in gerbil.

Previously, we revealed that Choto-san (Diao-teng-san in Chinese), a Kampo formula, is effective on vascular dementia clinically, and the hooks and stems of Uncaria sinensis (Oliv.) Havil., a medicinal plant comprising Chotosan, has a neuroprotective effect in vitro. In the present study, for the purpose of clarifying their effects in vivo, we investigated whether the oral administration of Choto-san extract (CSE) or U. sinensis extract (USE) reduces delayed neuronal death following ischemia/reperfusion (i/rp) in gerbils. Transient forebrain ischemia was induced by bilateral carotid artery occlusion for 4 min, and two doses (1.0% and 3.0%) of CSE or USE were dissolved in drinking water and provided to the gerbils ad libitum from 7 days prior to i/rp until 7 days after i/rp. It was found that 1.0% and 3.0% CSE treatments significantly reduced pyramidal cell death in the hippocampal CA1 region at 7 days post i/rp. Three percent USE treatment also inhibited pyramidal cell death significantly at 7 days after i/rp. Superoxide anion and hydroxyl radical scavenging activities of the homogenized hippocampus at 7 days after i/rp in the 1.0% CSE- and 3.0% USE-treated groups were significantly enhanced compared to those of control. Further, lipid peroxide and NO2-/NO3- levels of the homogenized hippocampus at 48h after i/rp in the 1.0% CSE- and 3.0% USE-treated groups were significantly lower than those of control. These results suggest that the oral administration of CSE or USE provides a protective effect against transient ischemia-induced delayed neuronal death by reducing oxidative damage to neurons.     

Morphological asymmetry of the abdomen and behavioral laterality in atyid shrimps

Morphological asymmetry and behavioral laterality in vertebrate species have been intensively studied in recent years, while comparable invertebrate studies are rare. Here we demonstrate asymmetry in the curvature of the abdomen and laterality in evasive responses for two atyid shrimps, Limnocaridina latipes and Neocaridina denticulata. The frequency distributions of the angle of the abdominal curvature in both species were discretely bimodal, suggesting that the two populations are composed of both left- and right-type individuals. In N. denticulata, behavioral analysis using high-speed filming illustrated that the escape direction for each individual, evoked by a sudden non-lateralized stimulus, was correlated with its abdominal curvature: left- (right-) type shrimp jumped back-leftward (-rightward) significantly more than often. A crossing experiment with N. denticulata indicated that the trait frequency in the F1 generation from two left-type parents differed significantly from that of the F1 generation from two right-type parents, and that the trait frequency for the F1 generation from parents of different laterality types did not deviate from random. That is, offspring laterality type is affected by the lateralities of the parents, indicating that abdominal dimorphism in shrimp is genetically derived. These results suggest that shrimp have an innate laterality that controls their escape direction, which in turn may affect prey-predator interactions in the aquatic community.     

Expression of nuclear receptor mRNA and liver X receptor-mediated regulation of ABC transporter A1 at rat blood-brain barrier

The aim of the present study was to investigate the expression of nuclear receptor mRNA and regulation of the expression of ATP-binding cassette (ABC) transporters by nuclear receptor agonists in rat brain capillary endothelial cells, which form the blood-brain barrier, by using rat brain capillary fraction from 8-week-old rats and a conditionally immortalized brain capillary endothelial cell line (TR-BBB13). RT-PCR analysis revealed that liver X receptor alpha and beta, retinoid X receptor alpha and beta and peroxisome proliferator-activating receptor alpha and beta mRNAs were expressed in the rat brain capillary endothelial cells and TR-BBB cells. In contrast, pregnane X receptor, farnesoid X receptor and constitutive androstane receptor were not detected. Furthermore, treatment with a liver X receptor agonist increased the ABCA1 mRNA level in TR-BBB13 cells, while ABCG2 mRNA expression was not affected. Treatment with a rat pregnane X receptor agonist did not affect the ABCB1 mRNA level in TR-BBB13 cells. These results demonstrate that the rat blood-brain barrier has an expressional regulation mechanism via sterol-related nuclear receptor, and indicate that the blood-brain barrier in 8-week-old rats lacks ABCB1 regulation via pregnane X receptor.     

The influence of gender on cardiac fibrosis induced by sympathetic stimulation

We examined the influence of sex steroids on cardiac effects of sympathetic agents in mice. The mice were divided into four groups: males, neutered males (N-males), females, and neutered females (N-females). Dobutamine (DOB; 2.5, 5.0, 10 microg/kg/min) or isoproterenol (ISO; 0.01, 0.02, 0.04 microg/kg/min) were given intravenously to compare the fractional shortening (FS). These mice received isoproterenol twice daily at a dose of 7.5 microg/g/day for 3 weeks. The rate of cardiac fibrosis was evaluated pathologically with Azan stain after 3 weeks of ISO. DOB and ISO significantly increased the FS in the male group, compared with other groups. There was no significant difference in FS between the female and N-female groups. Cardiac fibrosis significantly increased in the male group, compared with the N-male group. The female and N-female groups had increased cardiac fibrosis, compared with the male and N-male groups. These findings suggest that testosterone is one of the factors of modulation of the response to the sympathetic nervous system. Further study is needed to clarify the relationships between female sex steroids and cardiac fibrosis.