Syuiti Abe

Genetic population structure of chum salmon in the Pacific Rim inferred from mitochondrial DNA sequence variation

We examined the genetic population structure of chum salmon, Oncorhynchus keta, in the Pacific Rim using mitochondrial (mt) DNA analysis. Nucleotide sequence analysis of about 500 bp in the variable portion of the 5′ end of the mtDNA control region revealed 20 variable nucleotide sites, which defined 30 haplotypes of three genealogical clades (A, B, and C), in more than 2,100 individuals of 48 populations from Japan (16), Korea (1), Russia (10), and North America (21 from Alaska, British Columbia, and Washington). The observed haplotypes were mostly associated with geographic regions, in that clade A and C haplotypes characterized Asian populations and clade B haplotypes distinguished North American populations. The haplotype diversity was highest in the Japanese populations, suggesting a greater genetic variation in the populations of Japan than those of Russia and North America. The analysis of molecular variance and contingency χ2 tests demonstrated strong structuring among the three geographic groups of populations and weak to moderate structuring within Japanese and North American populations. These results suggest that the observed geographic pattern might be influenced primarily by historic expansions or colonizations and secondarily by low or restricted gene flow between local groups within regions. In addition to the analysis of population structure, mtDNA data may be useful for constructing a baseline for stock identification of mixed populations of high seas chum salmon.

Diagnosis of Synovial Sarcoma with the Reverse Transcriptase-polymerase Chain Reaction: Analyses of 84 Soft Tissue and Bone Tumors

The chimeric transcript SYT-SSX is generated as a result of reciprocal translocation t(X;18), which is the primary cytogenetic abnormality found in, and appears to be specific for, synovial sarcoma. We performed a reverse transcriptase-polymerase chain reaction (RT-PCR) for SYT-SSX transcripts in a series of 84 tumors (61 soft tissue tumors and 23 bone tumors), including a variety of histologic types, to assess its usefulness in molecular diagnosis. Ten synovial sarcomas, three tumors initially unclassified, and one malignant peripheral nerve sheath tumor contained the chimeric transcripts. A review of the original slides and additional examination showed that a diagnosis of synovial sarcoma was appropriate for these cases. Additionally, in situ hybridization with an SSX1 probe indicated that the chimeric transcripts exist not only in the cells of special components but also in cells showing a variety of histologic patterns. Therefore, RT-PCR can be considered a useful molecular biological technique that can provide objective evidence for diagnosis of synovial sarcoma. Northern blot analysis with an SSX1 probe also detected chimeric SYT-SSX transcripts in the synovial sarcoma cases. The additional smaller bands, however, were also detected in six peripheral primitive neuroectodermal tumors (pPNETs) and one embryonal rhabdomyosarcoma. In five of these pPNETs, other bands ranging in size from 2.0 to 2.2 kb were also found, and it seems possible that these bands might represent novel karyotypic aberrations and/or splicing variants of SSX.

Sex‐related spatial kin structure in a spring population of grey‐sided voles Clethrionomys rufocanus as revealed by mitochondrial and microsatellite DNA analyses

Polymerase chain reaction‐directed mitochondria (mt) and microsatellite DNA analyses were performed to examine the kin structure in a spring population of grey‐sided voles Clethrionomys rufocanus in Hokkaido, Japan. The spatial distribution of 81 voles in a trapping grid (about 1 ha) was estimated by using the catch‐mark‐release method. DNA samples were extracted from the toes clipped for individual identification. Maternal lineages of voles were unequivocally determined by the mtDNA haplotypes, as identified by nucleotide sequencing of the control region. Relatedness between individuals was estimated based on the genotype and allele frequencies at several microsatellite loci. Although the distribution of voles was uniform within the grid, neighbouring females were frequently from the same maternal lineage. Relatedness values between females correlated negatively with geographical distances. Combination of the two molecular markers revealed four clusters of closely related, matrilineal females in the population, whereas no such cluster was apparent in males. The present study first demonstrated a sex‐related spatial kin structure in a natural population of the grey‐sided vole.

Uniparental chromosome elimination in the early embryogenesis of the inviable salmonid hybrids between masu salmon female and rainbow trout male

Abstract.Chromosome elimination through chromosome loss and partial deletion is known to be one of the causes of embryonic inviability in some salmonid interspecific hybrids. Using fluorescence in situ hybridization and related techniques, including whole chromosome painting and comparative genomic hybridization, parental origin of eliminated chromosomes was identified in the inviable hybrids between masu salmon (Ms, Oncorhynchus masou) female and rainbow trout (Rb, O. mykiss) male at the early embryonic stage prior to death. In these hybrids, the haploid Rb chromosome number decreased to nearly half, whereas the Ms chromosomes were retained as one or occasionally two full haploid complements. The Rb chromosomes were also involved in the frequently observed fragments and micronuclei. Whereas the occurrence of fragments was constant throughout the observed period, chromosome loss occurred mainly from just after fertilization to the blastulae stage. In tissue sections and cell spreads of late blastula, some Rb chromosomes were trapped in the midzone from ana- to telophase, resulting in micronuclei at the subsequent interphase. Micronuclei and mitotic abnormalities were also observed in the androgenetic haploid hybrids. However, such abnormalities were seldom or never observed in the viable reciprocal hybrids. The present findings suggest that the paternal Rb chromosomes in the inviable hybrids are preferentially eliminated through mitotic abnormalities during early embryogenesis, owing to a possible incompatibility between the maternal Ms cytoplasm and paternal Rb genome.

Single nucleotide polymorphisms across a species' range: implications for conservation studies of Pacific salmon

Studies of the oceanic and near‐shore distributions of Pacific salmon, whose migrations typically span thousands of kilometres, have become increasingly valuable in the presence of climate change, increasing hatchery production and potentially high rates of bycatch in offshore fisheries. Genetics data offer considerable insights into both the migratory routes as well as the evolutionary histories of the species. However, these types of studies require extensive data sets from spawning populations originating from across the species’ range. Single nucleotide polymorphisms (SNPs) have been particularly amenable for multinational applications because they are easily shared, require little interlaboratory standardization and can be assayed through increasingly efficient technologies. Here, we discuss the development of a data set for 114 populations of chum salmon through a collaboration among North American and Asian researchers, termed PacSNP. PacSNP is focused on developing the database and applying it to problems of international interest. A data set spanning the entire range of species provides a unique opportunity to examine patterns of variability, and we review issues associated with SNP development. We found evidence of ascertainment bias within the data set, variable linkage relationships between SNPs associated with ancestral groupings and outlier loci with alleles associated with latitude.

Novel formation and amplification of the PAX7-FKHR fusion gene in a case of alveolar rhabdomyosarcoma.

Alveolar rhabdomyosarcomas frequently exhibit specific translocations, resulting in the fusion of the FKHR gene at 13q14 with either the PAX3 or PAX7 gene at 2q35 and Ip36, respectively. Comparative genomic hybridization revealed amplification at 13q14 and Ip36, suggesting amplification of the PAX7‐FKHR fusion gene in two cases of alveolar rhabdomyosarcoma. A PAX7‐FKHR fusion transcript was demonstrated in both cases by reverse transcription‐polymerase chain reaction followed by sequence analysis. In one case, amplification of the PAX7 gene and 3′‐ and 5′‐FKHR gene sequences was demonstrated by using interphase fluorescence in situ hybridization on tumor imprints. The colocalization, variable copy number, and distribution of signals from the three cosmids was consistent with amplification of these sequences on double minutes, which were present cytogenetically. Chromatin release studies suggested that the amplified sequences correlated with amplification of the PAX7‐FKHR fusion gene which resulted from the insertion of PAX7 sequences into the first intron of the FKHR gene, in keeping with the absence of cytogenetic evidence for derivative chromosomes. Genes Chromosom Cancer 17:7–13 (1996).

Molecular characterization of the genomic breakpoint junction in a t(11;22) translocation in Ewing sarcoma

Polymerase chain reaction (PCR)‐based nucleotide sequence analysis was performed in 12 cases of Ewing sarcoma on the cDNA and/or genomic DNA breakpoint regions of a t(11;22)(q24;q12), which joins the EWS gene located on chromosome 22 with the FLI1 gene located on chromosome 11, in order to understand the molecular mechanism of this translocation. Reverse transcriptase‐PCR on total tumor cell RNA from the examined cases showed five types of EWS‐FLI1 chimeric product, resulting from various junctions between EWS exon 7 or 10 with FLI1 exon 5, 6, or 8. Sequencing of the genomic fusion junctions of EWS‐FLI1 in seven cases showing three types of the chimeric cDNA products revealed that most of the breakpoint junctions shared common nucleotide(s) from both genes, and that the breakpoints in EWS introns 7 and 10 clustered within 100 bp and 300 bp, respectively. All the junctions were found to be flanked by various oligomers, among which a consensus sequence, 5′‐AGAAAARDRR‐3′, was found near the breakpoints of both genes in four cases, suggesting that these oligomers may have a functional significance in the genesis of t(11;22). In addition to these oligomers, sequences highly homologous to Alu repeats and/or eukaryotic topoisomerase II cleavage sites were located near, or flanked, or even encompassed, the breakpoints in most of the cases examined. Thus, these sequences may also mediate DNA double‐strand breakage and rejoining to generate the t(11;22). Genomic sequence analysis of both EWS‐FLI1 and FLI1‐EWS chimeric genes in three of the seven cases demonstrated a deletion and duplication of both EWS and FLI1 sequences in two cases and no gain or loss in one case. The present findings suggest that multiple mechanisms may be operative for the break and rejoining of the fragments of chromosomes 11 and 22 in the genesis of t(11;22), and that some of these translocations are asymmetric at the molecular level. Genes Chromosomes Cancer 25:6–15, 1999.

Null microsatellite alleles due to nucleotide sequence variation in the grey‐sided vole Clethrionomys rufocanus

Y . ISHIBASHI,* T. SAITOH,

Growth rate and sister chromatid exchange (SCE) incidence of bone marrow cells in Acute Myeloblastic Leukemia (AML)

S. ABE *+ and M. C. YOSHIDA *t * Chromosome Research Unit, Faculty of Science, Hokkaido University, North 10, West 8, Kita-Ku, Sapporo 060, Japan, t Laboratory of Cytogenetics, Graduate School of Environmental Earth Science, Hokkaido Unioersity, North 20, West 5, Kita-ku, Sapporo 060, Japan, and Wildlifi Management Laboratory, Hokkaido Research Centre, Forestry and Forest Products Research Institute, Hitsujigaoka 7 , Toyohira-ku, Sapporo 062, Japan

Establishment of a new continuous clear cell sarcoma cell line. Morphological and cytogenetic characterization and detection of chimaeric EWS/ATF-1 transcripts.

Abstract The sister chromatid exchange (SCE) incidence and growth kinetics have been studied by means of an in vitro bromodeoxyuridine (BrdU) chromosome labeling method in the bone marrow cells of 17 acute myeloblastic leukemia (AML) patients with only diploid cells at diagnosis, remission, and relapse of the disease. At diagnosis, the cells tended to exhibit a low SCE frequency as compared to that during remission. An increased SCE frequency was observed after chemotherapy during remission or relapse. At diagnosis and relapse, when leukemic blast cells predominated in the marrow, they were characterized by the predominance of cells that had undergone only one cell cycle after BrdU exposure. In contrast, the marrow cells during remission tended to resemble the control pattern of growth kinetics, with a predominance of cells undergoing second and third cell cycles in the presence of BrdU. These results suggest that the growth rate of leukemic and nonleukemic cells is different, and that chemotherapy can cause an increased SCE frequency in the marrow cells of AML patients irrespective of the state of the disease.