A molecular phylogeny of wild and cultivated Echinochloa in East Asia inferred from non-coding region sequences of trnT-L-F

The phylogenetic relationship among 30 accessions belonging to nine species of the genus Echinochloa Beauv. was studied on the basis of the sequence of three non-coding regions ( trn T-L, trn L-F intergenic spacers, and trn L intron) of chloroplast DNA (cpDNA). A strict consensus parsimonious tree of the three most parsimonious trees derived from 25 polymorphic sites (six indels and 19 substitutions) in the total sequences, ranging from 1715–1760 bp, represented five groups: (i) Echinochloa oryzicola Vasing. and Echinochloa stagnina Beauv. from Thailand; (ii) Echinochloa crus-galli Beauv. complex; (iii) Echinochloa crus-pavonis Schult; (iv) Echinochloa colonum Link. and Echinochloa frumentacea Link.; and (v) the African species, Echinochloa obtusiflora Stapf and Echinochloa stagnina . Japanese barnyard millet ( Echinochloa esculenta H. Scholz) and various weedy varieties of E. crus-galli and Echinochloa oryzoides Fritsch had quite similar sequences and formed the E. crus-galli complex, which was characterized by six substitutions. A cultivated form of E. oryzicola (Mosuo barnyard millet) and various morphological and agronomical forms of E. oryzicola were characterized by two indels. Indian barnyard millet ( E. frumentacea ) and its wild counterpart ( E. colonum ) were characterized by five substitutions. Domestication as millets and adaptation to paddy environments as mimic weeds might occur after the divergence of species in the Asian Echinochloa .     

Na?ve-like conversion enhances the difference in innate in vitro differentiation capacity between rabbit ES cells and iPS cells

Quality evaluation of pluripotent stem cells using appropriate animal models needs to be improved for human regenerative medicine. Previously, we demonstrated that although the in vitro neural differentiating capacity of rabbit induced pluripotent stem cells (iPSCs) can be mitigated by improving their baseline level of pluripotency, i.e., by converting them into the so-called “naïve-like” state, the effect after such conversion of rabbit embryonic stem cells (ESCs) remains to be elucidated. Here we found that naïve-like conversion enhanced the differences in innate in vitro differentiation capacity between ESCs and iPSCs. Naïve-like rabbit ESCs exhibited several features indicating pluripotency, including the capacity for teratoma formation. They differentiated into mature oligodendrocytes much more effectively (3.3–7.2 times) than naïve-like iPSCs. This suggests an inherent variation in differentiation potential in vitro among PSC lines. When naïve-like ESCs were injected into preimplantation rabbit embryos, although they contributed efficiently to forming the inner cell mass of blastocysts, no chimeric pups were obtained. Thus, in vitro neural differentiation following naïve-like conversion is a promising option for determining the quality of PSCs without the need to demonstrate chimeric contribution. These results provide an opportunity to evaluate which pluripotent stem cells or treatments are best suited for therapeutic use.     

Gene dropping analysis of founder contributions in a closed Japanese black cattle population

Gene dropping simulation was applied to Japanese Black cattle population in Hyogo prefecture, to examine the survivals of alleles originated from founder animals. In the analysis, unique alleles were assigned to founders, and the genotypes of all descendants along the actual pedigree were generated through Monte Carlo simulation following Mendelian segregation rules. By replicating this process 10 000 times, the distribution of frequencies of alleles from each founder was estimated. From the distribution, several quantities useful for the management of genetic diversity, such as the probability of allele extinction and the probability of alleles surviving at a critically low frequency were derived. The materials used were 68 781 animals born in 1955–1998 and their pedigree records traced back to the population in 1937 or before. The expected number of alleles retained in the population drastically decreased during the analyzed period, and reached to 57.9 in the population of 1998, which was only 3.3% of the total number of alleles assigned to founders. Detailed analysis of major founders with relatively high genetic contributions to the current population revealed that alleles from most of the major founders are now at high risk of future extinction. These results strongly suggest that for the management of genetic diversity, the genetic contributions of founders are not fully informative, and emphasize the importance of the detection of live animals having founder alleles with high extinction possibilities.     

Oxytocin Cells in the Supraoptic Nucleus Receive Excitatory Synaptic Inputs from the Contralateral Supraoptic and Paraventricular Nuclei in the Lactating Rat

The present experiments were undertaken to examine whether oxytocin cells in the supraoptic nucleus receive synaptic inputs from the contralateral supraoptic nucleus or paraventricular nucleus. Using urethane-anesthetized lactating rats, extracellular action potentials were recorded from single oxytocin or vasopressin cells in the supraoptic nucleus. Electrical stimulation was applied to the contralateral supraoptic nucleus or paraventricular nucleus, and responses of oxytocin or vasopressin cells were analyzed by peri-stimulus time histogram or by change in firing rate of oxytocin or vasopressin cells. Electrical stimulation of the contralateral supraoptic nucleus or paraventricular nucleus did not cause antidromic excitation in oxytocin or vasopressin cells but caused orthodromic responses. Although analysis by peri-stimulus time histogram showed that electrical stimulation of the contralateral supraoptic nucleus or paraventricular nucleus caused orthodromic excitation in both oxytocin and vasopressin cells, the proportion of excited oxytocin cells was greater than that of vasopressin cells. Train stimulation applied to the contralateral supraoptic nucleus or paraventricular nucleus at 10 Hz increased firing rates of oxytocin cells and decreased those of vasopressin cells. The results of the present experiments suggest that oxytocin cells in the supraoptic nucleus receive mainly excitatory synaptic inputs from the contralateral supraoptic nucleus and paraventricular nucleus. Receipt these synaptic inputs to oxytocin cells may contribute to the synchronized activation of oxytocin cells during the milk ejection reflex.     

Age‐dependent distribution of juvenile southern bluefin tuna (Thunnus maccoyii) on the continental shelf off southwest Australia determined by acoustic monitoring

Juvenile southern bluefin tuna (Thunnus maccoyii, SBT) were monitored in nearshore waters off southwest Australia using acoustic tagging and monitoring over five austral summers (2002/2003–2006/2007) to determine patterns in age‐based distribution of SBT. A total of 20–70 receivers were deployed in early December along one to three cross‐shelf transects and at three inshore topographic features (lumps) where SBT are known to occur; and a total of 59–84 juvenile SBT (41–90 cm fork length) were tagged and released each year. After several months, receivers were recovered, and data extracted. In 2002/2003 and 2003/2004, 2‐yr‐old SBT were detected more frequently in nearshore areas than did 1‐yr old fish. Similarly in 2004/2005 and 2006/2007, it was the larger 1‐yr‐old SBT that were detected more frequently at inshore lumps (>85% of detections) while small 1‐yr‐old SBT were detected more widely over the study area. In 2005/2006, although large 1‐yr‐old SBT were still detected more frequently at inshore lumps than small 1‐yr old SBT, the percentage of all detections at lumps was lower at 31.5%, indicating wider distribution of both small and large age‐1 fish. The observed age‐dependent distribution pattern may be enhanced by the distribution of prey, which disperse or concentrate depending on the local oceanography.     

Interannual variation in summer habitat utilization by juvenile southern bluefin tuna (Thunnus maccoyii) in southern Western Australia

The spatial habitat utilization of juvenile southern bluefin tuna in southern Western Australia was investigated using automated acoustic receivers with acoustic transmitters implanted in tagged fish during three austral summers (2004/2005, N = 79 fish, 2005/2006, N = 81, 2006/2007, N = 84). Seventy acoustic receivers were deployed at three cross-shelf lines and three coastal topographic features (lumps) between December and May. We observed markedly different patterns of habitat utilization between the three seasons: (i) aggregation at lumps in 2004/2005 and 2006/2007, and (ii) wide distribution over the continental shelf (i.e., few occurring at lumps) in 2005/2006. Vertical profile by conductivity-temperature-depth casts showed these spatial shifts were caused by interannual changes in the presence of sub-Antarctic water. The sub-Antarctic water was present in the subsurface layer close to the continental slope only during 2005/2006, and the area had higher chlorophyll-a concentrations than the coastal areas, including at the lumps. These environmental characters, related to the nutrient rich sub-Antarctic water, appear to have a strong influence on fish distributions in 2005/2006, and may occur generally during La Niña events. Interannual fluctuations in habitat utilization will influence detection of fish in recruitment monitoring surveys and thus bias the resulting juvenile abundance indices.     

Molecular Characterization of <Emphasis Type="Italic">Bean yellow mosaic virus </Emphasis>from Vegetatively Propagated Dwarf <Emphasis Type="Italic">Gentiana </Emphasis>Plants

The causative virus (isolate No. 4) of gentian (Gentiana spp.) mosaic, which had been identified previously as Clover yellow vein virus (C1YVV) on the basis of host range and serological reactions, was re-identified as Bean yellow mosaic virus (BYMV) on the basis of the nucleotide sequences of the gene for the coat protein (CP) and the 3′-noncoding region, as well as the predicted amino acid sequence of CP. Received 16 April 2002/ Accepted in revised form 19 June 2002     

Molecular identification of Echinochloa oryzicola Vasing. and E. crus-galli (L.) Beauv. using a polymerase chain reaction–restriction fragment length polymorphism technique

Polymerase chain reaction (PCR) and polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) techniques were applied for establishing the reliable practice in identification of Echinochloa oryzicola Vasing. and E. crus-galli (L.) Beauv. (barnyardgrass). Total DNA was extracted from 18 accessions and 86 individuals of E. oryzicola , 33 accessions and 140 individuals of E. crus-galli var. crus-galli , 23 individuals of E. crus-galli var. praticola , and six individuals of E. crus-galli var. formosensis that were collected from Japan. A partial region of intergenetic spacer between trn T and trn L, and an intron of trn L were amplified separately using a trn-a and trn-b1 primer set, and a trn-c and trn-d primer set, respectively. All individuals of E. oryzicola showed the same fragment amplified by the trn-a and trn-b1 primer set. The fragment was 481 bp in length, and was undigested by Eco R I, whereas all individuals of E. crus-galli , including three botanical varieties, showed the same fragment with a 449-bp length. The fragment was digested by Eco R I into two fragments (178 and 271 bp). The fragment amplified by the trn-c and trn-d primer set in all individuals of E. oryzicola was digested by Alu I into two fragments (174 and 452 bp), but undigested by Dra I. In contrast, the fragment amplified by the trn-c and trn-d primer set in all individuals of E. crus-galli was digested by Dra I into two fragments (134 and 487 bp), but undigested by Alu I. There was no intraspecific variation in these regions; thus, these two species are easily identifiable by using our method.     

Pedigree analysis of genetic subdivision in a population of Japanese Black cattle

Twenty‐five subpopulations (i.e. populations of prefectures) of more than 2000 Japanese Black cows younger than or equal to 10 years of age were analyzed to evaluate the genetic relationships in the current population. The total number of cows analyzed was 392 346 and their pedigrees were traced back to 1944 or before. Using the pedigree records, the genetic relationships among the subpopulations were estimated by the two different measurements: (i) the average additive relationship coefficients and (ii) Nei's standard genetic distances. Principal component analysis (PCA) was performed to the matrix of the average additive relationship coefficients, and the factor loadings of subpopulations were plotted on the plane to visualize the genetic configuration of subpopulations. To understand the grouping process of the subpopulations, cluster analysis was applied to the matrix of the Nei's genetic distances, and a dendrogram was constructed. There was a high consistency between the results from PCA and cluster analysis. Eight subpopulations with relatively low migration rates showed their unique genetic compositions, and the other 17 subpopulations with high migration rates formed a single cluster. The major cause of the genetic similarity among the 17 subpopulations was inferred to be the strong genetic influence from one subpopulation (Hyogo prefecture) with prominent characteristics for meat quality.