Population structure and demographic history for year cohort dynamics of landlocked ayu Plecoglossus altivelis altivelis in dam reservoir of Japan.

Ayu Plecoglossus altivelis altivelis is a valuable osmeroid species for inland fishery in Japan. It is classified into two ecological forms of amphidromous migrating between rivers and sea and landlocked migrating between rivers and lakes or dam reservoirs. The number of dams and their reservoirs has remarkably increased in the twenty-first century under climate change, because of their respective roles in hydropower generation with negligible carbon emissions and in flood control.

Stock assessment of landlocked ayu Plecoglossus altivelis altivelis in Japan through length-based models.

Ayu Plecoglossus altivelis altivelis is a key commercially and culturally important freshwater osmeroid in Japan. Its native population is mostly an amphidromous form migrating between rivers and the sea, and not only native but also artificially landlocked forms are found in lakes and dam reservoirs. This study was undertaken to execute population feasibility and maximum sustainable yield (MSY) analysis of an artificially landlocked form of ayu during January 2018 to December 2020 in the Haidzuka reservoir and its connected Tabusa River, western Japan.

Stochastic optimal switching model for migrating population dynamics.

An optimal switching control formalism combined with the stochastic dynamic programming is, for the first time, applied to modelling life cycle of migrating population dynamics with non-overlapping generations. The migration behaviour between habitats is efficiently described as impulsive switching based on stochastic differential equations, which is a new standpoint for modelling the biological phenomenon. The population dynamics is assumed to occur so that the reproductive success is maximized under an expectation.

A simple and reliable method for DNA extraction from bivalve mantle.

A simple and reliable method was developed for extracting genomic DNA from preserved mantle tissues of Pacific oyster Crassostrea gigas for reproducible PCR amplification. The method was based on destruction of the tissue using Proteinase K, Chelex 100 resin, detergents, and urea, followed by preferential capturing of genomic DNA with silica particles. Approximately 5 mg of mantle tissue provided a sufficient quality and quantity of DNA for several hundreds of PCR reactions amplifying the hypervariable mitochondrial DNA intergenic spacer, which is a useful genetic marker for population structure analysis of Pacific oyster.

A novel mitochondrial intergenic spacer reflecting population structure of Pacific oyster.

Nucleotide sequence divergence in a novel major mitochondrial DNA intergenic spacer (IGS) of Pacific oyster Crassostrea gigas was analyzed for 29 cultured individuals within the Goseong population (Korea). A total of 7 variable sites were detected within the IGS, and the relative frequency of nucleotide alteration was determined to be 1.16%;.

Molecular identification of hairtail species (Pisces: Trichiuridae) based on PCR-RFLP analysis of the mitochondrial 16S rRNA gene.

A rapid PCR-RFLP analysis was designed to identify 3 closely related species of hairtails: Trichiurus lepturus, T. japonicus, and Trichiurus sp. 2, basing on partial sequence data (600 bp) of the mitochondrial DNA encoding the 16S ribosomal RNA (16S rRNA) gene.

Rapid PCR-RFLP method for discrimination of imported and domestic mackerel.

With the ever-decreasing domestic fishery catch of Japanese mackerel Scomber japonicus, alternative Atlantic mackerel Scomber scombrus has been increasingly imported and currently accounts for approximately 34% of mackerel consumption in Japan. As there is no morphologic difference between the species after removal of their skin, not only fresh and frozen fillets but also processed seafood of S. scombrus are frequently marketed with mislabeling as S.

A novel type of myofibril-bound serine protease from white croaker (Argyrosomus argentatus).

Myofibril-bound serine protease (MBSP) was purified from the myofibril fraction of white croaker (Argyrosomus argentatus) muscle and its enzymatic properties were compared with other fish MBSPs. White croaker MBSP was extracted by the heat treatment of myofibrils and then purified by a series of column chromatographies on Q-Sepharose, Sephacryl S-300, hydroxyapatite and Benzamidine Sepharose. The purified MBSP migrated as a single protein band at 67 kDa in SDS-PAGE under both reducing and non-reducing conditions.

Sequence polymorphism in a novel noncoding region of Pacific oyster mitochondrial DNA.

Nucleotide sequence polymorphism in a 641-bp novel major noncoding region of mitochondrial DNA (mtDNA-NC) of the Pacific oyster Crassostrea gigas was analysed for 29 cultured individuals within the Goseong population. A total of 30 variable sites were detected, and the relative frequency of nucleotide alteration was determined to be 4.68.

Identification of gadoid species (Pisces, Gadidae) by PCR-RFLP analysis.

A rapid PCR-RFLP analysis was optimized to identify the presence of 3 closely related gadoid fish species: Alaska pollack Theragra chalcogramma, Pacific cod Gadus macrocephalus and Atlantic cod Gadus morhua in commercial seafood products. Gadoid universal primers were designed for PCR amplification of a 558-bp fragment encoding the mitochondrial cytochrome b gene. Without purification of the PCR products, double digestion with Eco32I and Eco105I restriction enzymes generated reproducible species-specific restriction patterns visualizing 3 fragments (106 bp, 161 bp and 291 bp) in Alaska pollack and 2 fragments (106 bp and 452 bp) in Pacific cod, whereas no cleavage was observed in Atlantic cod.

PCR-RFLP analysis of nuclear nontranscribed spacer for mackerel species identification.

Scomber mackerel have been marketed in fresh and frozen forms and as processed seafood worldwide, and three species of Japanese mackerel S. japonicus, Pacific mackerel S. australasicus, and Atlantic mackerel S.

Genetic relationship between cultured populations of Pacific oyster revealed by RAPD analysis.

We developed random amplified polymorphic DNA (RAPD) analysis for the assessment of the genetic relationship between cultured populations of the Pacific oyster Crassostrea gigas Thunberg in Hiroshima and Goseong, the largest oyster farming areas in Japan and Korea, respectively. Of 25 arbitrary primers comprising decamer nucleotides of random sequences, polymerase chain reaction amplifications with 5 different primers gave reproducible electrophoretic patterns. A total of 49 RAPD markers were clearly identified for the Hiroshima and Goseong populations, and 46 markers were polymorphic presenting mean polymorphism rates of the respective populations at 92.

Relationship between gyrA mutations and quinolone resistance in Flavobacterium psychrophilum isolates.

Flavobacterium psychrophilum is the causative agent of the fish diseases called bacterial cold-water disease and rainbow trout fry syndrome. It has been reported that some isolates of F. psychrophilum are resistant to quinolones; however, the mechanism of this quinolone resistance has been unexplained.

Genotyping of Flavobacterium psychrophilum using PCR-RFLP analysis.

Genetic variability among 242 strains of Flavobacterium psychrophilum was characterized using polymerase chain reaction (PCR) followed by restriction fragment length polymorphism (RFLP) analysis. Universal Primers GYR-1 and GYR-1R, which were designed to amplify the gyrase subunit B gene (gyrB), yielded a 1178 bp PCR product encoding gyrB and a 290 bp PCR product of anonymous DNA from all F. psychrophilum strains tested.

Development of novel microsatellite DNA markers from the Pacific oyster Crassostrea gigas.

We document the potential of novel microsatellites as a genetic tool in furthering our understanding of the Crassostrea gigas genetic structure. From the microsatellite-enriched libraries we constructed, 123 repeat regions that had sufficient sequence information to design polymerase chain reaction primer sets were isolated. From these, 9 primer pairs were screened in a C.

Flexprep: scale-flexible rapid plasmid preparation for analysis of recombinant clones.

A scale-flexible and cost-efective protocol for plasmid preparation is described to cover miniprep and midiprep scale work in a microcentriguge format for analysis of recombinant clones, this protocol relies on a modified alkaline lysis of Escherichia coli cells and subsequent purification of plasmid DNA with no organic extraction and alcohol precipitation. It can process up to 20 mL of E. coli cells carrying 3-10 kbp plasmid vectors in < 10 min.