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Suyama Y, Kawamuro K, Kinoshita I, Yoshimura K, Tsumura Y, Takahara H. DNA sequence from a fossil pollen of Abies spp. from Pleistocene peat. Genes Genet Syst 1996; 71:145-9. [PMID: 8828176 DOI: 10.1266/ggs.71.145] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
DNA was amplified from individual fossil pollen grains of Abies spp. (Pinaceae), which have been detected from Pleistocene peaty deposits (at least 150,000 years old). To identify the species of the fossil pollen by DNA analysis, the region indicating the species-specific sequence was searched among extant Abies species and the spacer region between rrn5 and trnR in chloroplast DNA was sequenced for four grains of the fossil pollen. Three pollen samples produced the same sequence as extant Abies species. The sequence for the remaining sample differed from that of extant Abies by one substitution. This study showed not only a successful DNA analysis from a single grain of fossil pollen but also a new method to identify the species of fossil pollen for the pollen analysis field.
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Nakamura Y, Tsumura Y, Tonogai Y, Shibata T, Ito Y. Differences in behavior among the chlorides of seven rare earth elements administered intravenously to rats. FUNDAMENTAL AND APPLIED TOXICOLOGY : OFFICIAL JOURNAL OF THE SOCIETY OF TOXICOLOGY 1997; 37:106-16. [PMID: 9242583 DOI: 10.1006/faat.1997.2322] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Differences in behavior among the chlorides of seven rare earth elements (REEs)-yttrium (Y), cerium (Ce), and praseodymium (Pr) (light REEs); europium (Eu) and dysprosium (Dy) (medium REEs); ytterbium (Yb) and lutetium (Lu) (heavy REEs)-were investigated through intravenous administration of the REEs to rats. (1) Distributions of REEs and mineral concentrations in the organs on Day 1 were investigated at low and high doses (9-10 and 18-20 mg REE/kg, or 56-66 and 112-132 mumol REE/kg). More than 78% of the REEs administered was distributed into liver, bone, and spleen. High doses of Y, Eu, and Dy markedly increased the accumulation of REEs in spleen and lungs as well as the concentration of Ca in liver, spleen, and lungs. (2) The distribution patterns of REEs and changes in Ca concentrations in major organs over time were investigated by the administration of Pr, Eu, Dy, Yb (low dose), and Y (high dose). REEs disappeared from the blood within 1 day but were retained in the organs for a long time. The percentages of the doses of Y, Eu, Dy, and Yb found in the liver were highest at 8 hr to 2 days, then decreased gradually; hepatic Pr levels, however, remained high. Changes in Ca concentrations in liver, spleen, and lungs were in accordance with those of REEs. (3) Severe hepatotoxicity was observed after administration of Ce and Pr; fatty liver, jaundice, and elevated serum GOT and GPT levels were most prominent on Day 3. Therefore, we hypothesized that REE chlorides might be categorized into three groups according to their ionic radii (light REEs, Y and medium REEs, and heavy REEs) and from their behavior, i.e., distribution pattern, Ca-accumulating action, and hepatotoxicity.
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Tsumura Y, Ohba K, Strauss SH. Diversity and inheritance of inter-simple sequence repeat polymorphisms in Douglas-fir (Pseudotsuga menziesii) and sugi (Cryptomeria japonica). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1996; 92:40-5. [PMID: 24166114 DOI: 10.1007/bf00222949] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/1995] [Accepted: 05/26/1995] [Indexed: 05/20/2023]
Abstract
We studied inter-simple sequence repeat (ISSR) polymorphism and inheritance in Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco] and sugi (Cryptomeria japonica D. Don) megagametophytes using primers that anneal to simple repeats of various lengths, sequences, and non-repetitive motifs at the 5' and 3' ends. Products were visualized on agarose gels with ethidium bromide staining. More than 60% of the 96 primers tested gave interpretable banding patterns in both Douglas-fir and sugi, and the useful primers were in complete agreement among species. Dinucleotide repeat primers were the majority of those tested, and gave all of the useful banding patterns. The 24 best primers were used for segregation studies, yielding a total of 77 loci distributed among two Douglas-fir families and one sugi family. Approximately 90% of the 24 primers showed polymorphism within at least one of the three families. The average number of variable loci per primer was 1.6. Primers based on (AG) n repeats gave the largest number of polymorphic loci; 16 primer-family combinations yielded 24 segregating loci. However, primer based on (GT) n repeats gave the most loci per primer studied (mean of 2.0). All markers displayed apparent dominance (band presence vs absence), and all but three segregation ratios (4%) fit Mendelian expectations: Because they employ longer primers than do RAPDs, have a high degree of polymorphism, conform well to Mendelian expectations, and do not require use of acrylamide gels for analysis, ISSRs may be useful markers for PCR-based genome maps and population studies of conifers.
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Tsumura Y, Ishimitsu S, Kaihara A, Yoshii K, Nakamura Y, Tonogai Y. Di(2-ethylhexyl) phthalate contamination of retail packed lunches caused by PVC gloves used in the preparation of foods. FOOD ADDITIVES AND CONTAMINANTS 2001; 18:569-79. [PMID: 11407756 DOI: 10.1080/02652030120071] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Plasticizer contamination of foods sold in retail packed lunches and set lunches in restaurants was determined by GC/MS. The phthalate esters were as follows: diethyl, dipropyl, dibutyl, dipentyl, dihexyl, butylbenzyl, dicyclohexyl, di(2-ethylhexyl), dioctyl, diisooctyl (mixture of isomers) and diisononyl (mixture). Di(2-ethylhexyl) adipate was also determined. Sixteen packed lunches and ten set lunches were analysed, and in all samples the concentration of di(2-ethylhexyl) phthalate (DEHP) was the highest, at 0.80-11.8 mg/kg in packed lunches and 0.012-0.30 mg/kg in set lunches. The DEHP content of five packed lunches exceeded 1.85 mg, which is the EU tolerable daily intake (TDI) for a person of 50 kg body weight. Foodstuffs that were components of the packed lunches were taken from the factory at each step of preparation and phthalates were determined. For example, chicken contained 0.08 mg/kg DEHP when uncooked, 13.1 mg/kg after frying and 16.9 mg/kg after packing. Disposable PVC gloves used in the preparation of foods were apparently the source of high DEHP concentrations. The gloves used during cooking or packaging were sprayed with 68% (w/w) ethanol to sterilize them. PVC gloves from the factory contained 22 or 41% by weight of DEHP. To confirm the link with the contamination problem, samples of boiled rice, croquette and boiled dry radish were handled in the laboratory with PVC gloves containing 30% (w/w) DEHP. DEHP migration levels of 0.05 mg/kg in rice or 0.33 mg/kg in croquette, and 11.1 mg/kg in radish were found. The alcohol sprayed onto the gloves increased the migration of DEHP to 2.03 mg/kg in rice, 2.45 mg, kg in croquette, and 18.4 mg/kg in radish.
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Tomaru N, Takahashi M, Tsumura Y, Takahashi M, Ohba K. Intraspecific variation and phylogeographic patterns of Fagus crenata (Fagaceae) mitochondrial DNA. AMERICAN JOURNAL OF BOTANY 1998. [PMID: 21684944 DOI: 10.2307/2446531] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Mitochondrial (mt) DNA variation in Japanese beech, Fagus crenata (Fagaceae), was studied in 17 populations distributed throughout the species' range. Total genomic DNA of samples from single trees representing each of 12 populations were digested with 18 restriction enzymes and hybridized with three probes containing coxI, coxIII, and atpA gene sequences. Thirty-four of the 54 enzyme/probe combinations showed polymorphisms and all the individuals were subsequently analyzed with six combinations of three probes and two enzymes. Restriction fragment length polymorphisms were evident around all three genes, allowing the identification of eight distinct haplotypes. Haplotype diversity within the populations was found to be very low (HS = 0.031), but population differentiation to be much higher (GST = 0.963). The mtDNA variation was strikingly different from allozyme variation (HS = 0.209; GST = 0.039). Gene flow for maternally inherited mtDNA should be restricted to seed dispersal while nuclear gene flow occurs by both seed and pollen dispersal. Therefore, the difference in the variation between mtDNA and allozymes may be largely a result of the much higher rate of gene flow associated with pollen dispersal than with seed dispersal. The mtDNA variation displayed strong geographic structure, which may reflect the species' distribution in the last glacial maximum and subsequent colonization, and probably also reflects intraspecific phylogeography of the species.
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Tsuda Y, Nakao K, Ide Y, Tsumura Y. The population demography ofBetula maximowicziana, a cool-temperate tree species in Japan, in relation to the last glacial period: its admixture-like genetic structure is the result of simple population splitting not admixing. Mol Ecol 2015; 24:1403-18. [DOI: 10.1111/mec.13123] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 02/17/2015] [Accepted: 02/18/2015] [Indexed: 11/29/2022]
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57 |
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Konuma A, Tsumura Y, Lee CT, Lee SL, Okuda T. Estimation of gene flow in the tropical-rainforest tree Neobalanocarpus heimii (Dipterocarpaceae), inferred from paternity analysis. Mol Ecol 2000; 9:1843-52. [PMID: 11091320 DOI: 10.1046/j.1365-294x.2000.01081.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pollen flow and population genetic structure among 30 potentially flowering individuals of Neobalanocarpus heimii, a tropical emergent tree, were investigated in a lowland tropical rainforest of Malaysia using microsatellite polymorphism. The 248 offspring in the vicinity of five reproductive trees of the 30 potentially flowering trees were used in paternity analysis for pollen-flow study. Four primer pairs, developed in different species of dipterocarps, were adopted to detect microsatellite polymorphism. Based upon microsatellite polymorphism, pollen flow and seed migration were detected. Pollen-flow events of more than 400 m were observed directly, based on paternity analysis in the study plot. The estimated average mating distance of the five reproductive trees was 524 m. This result suggests that reproduction of this species is mediated by a long-distance pollinator. The haplotypes of some offspring were not compatible with the nearest reproductive tree. Thus, the results suggest that some seeds are dispersed by a seed dispersal vector. Investigation of genetic structure showed significant and negative correlation of genetic relatedness and spatial distances between the 30 potentially flowering trees, but this correlation was weak. We suggest that long-distance gene flow and seed migration are responsible for the poorly developed genetic structure of this species.
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Ujino T, Kawahara T, Tsumura Y, Nagamitsu T, Yoshimaru H, Ratnam W. Development and polymorphism of simple sequence repeat DNA markers for Shorea curtisii and other Dipterocarpaceae species. Heredity (Edinb) 1998; 81 ( Pt 4):422-8. [PMID: 9839438 DOI: 10.1046/j.1365-2540.1998.00423.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nine simple sequence repeat (SSR) markers were developed from Shorea curtisii using two different methods. One SSR locus was isolated by the commonly used method of screening by colony hybridization, and the other eight loci were isolated by a vectorette PCR method. Primer pairs were designed based on the sequences of all these SSR loci. Analysis of 40 individuals of S. curtisii from natural forest in Malaysia revealed that all SSR loci were polymorphic. Four SSR markers, Shc01, Shc04, Shc07 and Shc09, were highly polymorphic. We have also tested the applicability of these SSR printers to other species of Dipterocarpaceae using PCR amplification. Because the flanking region sequences of the S. curtisii SSRs were well conserved within this family, the SSR primers for S. curtisii can be applied to almost all species of Dipterocarpaceae.
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Kajita T, Kamiya K, Nakamura K, Tachida H, Wickneswari R, Tsumura Y, Yoshimaru H, Yamazaki T. Molecular phylogeny of Dipetrocarpaceae in Southeast Asia based on nucleotide sequences of matK, trnL intron, and trnL-trnF intergenic spacer region in chloroplast DNA. Mol Phylogenet Evol 1998; 10:202-9. [PMID: 9878231 DOI: 10.1006/mpev.1998.0516] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To obtain a refined molecular phylogeny of dipterocarp species in Southeast Asia, nucleotide sequences of matK, the intron of trnL, and intergenic spacer region between trnL and trnF in chloroplast DNA were determined in 16 species throughout 10 genera. In the resultant trees Southeast Asian dipterocarp species were divided into two clusters. One cluster consisted of Anisoptera, Vatica, Cotylelobium, and Upuna, all with the base chromosome number of x = 11. The second cluster consisted of Hopea, Shorea, Neobalanocarpus, Dryobalanops, Parashorea, and Dipterocarpus, mostly with the base chromosome number of x = 7. Dipterocarpus was the only genus that had the base chromosome number x = 11 in the latter cluster. This result suggests that the chromosome number changed from x = 11 to x = 7 after Dipterocarpus branched in the latter cluster. Other evolutionary changes of morphological characters are also discussed.
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Tsumura Y, Ishimitsu S, Saito I, Sakai H, Kobayashi Y, Tonogai Y. Eleven phthalate esters and di(2-ethylhexyl) adipate in oneweek duplicate diet samples obtained from hospitals and their estimated daily intake. ACTA ACUST UNITED AC 2001; 18:449-60. [PMID: 11358187 DOI: 10.1080/02652030117484] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Plasticizers in duplicate diet samples obtained over 1 week were analysed in order to estimate daily intake. The phthalate esters were as follows: diethyl, dipropyl, dibutyl, dipentyl, dihexyl, butylbenzyl, dicyclohexyl, di(2-ethylhexyl), dioctyl, diisooctyl (mixture of isomers) and diisononyl (mixture). Di(2-ethylhexyl) adipate was also determined. Homogenized samples of composite meals were extracted with acetonitrile, lipids were removed by extraction into n-hexane and the acetonitrile layer was cleaned using Florisil and Bondesil PSA dual layer column. Phthalates were determined by GC/MS (SIM). Phthalate recovery from the fortified food mixture by this method was 62.5-140.8%. Quality assurance as assessed by three laboratories indicated coefficient of variance in the levels of detected phthalates in same lot samples as below 10%. Detection limits were 0.1-23 ng/g for each phthalate. One-week duplicate diet samples provided by three hospitals in three remote prefectures of Japan were analysed as individual meals. In all 63 samples, DEHP was present at the highest level among all phthalates in the range 10-4400 ng/g. The intake of plasticizers estimated from all samples was 519 microg DEHP/day, 86 microg DEHA/day, 65 microg DINP/day, and 4.7 microg BBP/day. Calculated DEHP in 2-day samples out of 21 days exceeded EU TDI for a person of 50 kg body weight (1850 microg per day). Disposable PVC gloves used during the preparation of meals were suspected as the source of the high DEHP content. One-day intake of the other phthalates and DEHA was below 7% of TDI in all cases. High concentrations of DEHP (5990 ng/g) was found in baby food used in quality assurance work. The source of contamination was the PVC-tube used during production and was effectively reduced by replacing the tube by one made of stainless steel.
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Tsumura Y, Uchiyama K, Moriguchi Y, Ueno S, Ihara-Ujino T. Genome scanning for detecting adaptive genes along environmental gradients in the Japanese conifer, Cryptomeria japonica. Heredity (Edinb) 2012; 109:349-60. [PMID: 22929151 DOI: 10.1038/hdy.2012.50] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Local adaptation is important in evolutionary processes and speciation. We used multiple tests to identify several candidate genes that may be involved in local adaptation from 1026 loci in 14 natural populations of Cryptomeria japonica, the most economically important forestry tree in Japan. We also studied the relationships between genotypes and environmental variables to obtain information on the selective pressures acting on individual populations. Outlier loci were mapped onto a linkage map, and the positions of loci associated with specific environmental variables are considered. The outlier loci were not randomly distributed on the linkage map; linkage group 11 was identified as a genomic island of divergence. Three loci in this region were also associated with environmental variables such as mean annual temperature, daily maximum temperature, maximum snow depth, and so on. Outlier loci identified with high significance levels will be essential for conservation purposes and for future work on molecular breeding.
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Journal Article |
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Tsumura Y, Ishimitsu S, Saito I, Sakai H, Tsuchida Y, Tonogai Y. Estimated daily intake of plasticizers in 1-week duplicate diet samples following regulation of DEHP-containing PVC gloves in Japan. FOOD ADDITIVES AND CONTAMINANTS 2003; 20:317-24. [PMID: 12775472 DOI: 10.1080/0265203031000122021] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Duplicate hospital diet samples obtained over 1 week in 2001 were analysed to estimate the daily intake of plasticizers and the results were compared with those obtained in 1999. The plasticizers quantified in this study were: dibutyl phthalate, butylbenzyl phthalate (BBP), di(2-ethylhexyl) phthalate (DEHP), diisononyl phthalate (DINP), di(2-ethylhexyl) adipate (DEHA), diisononyl adipate (DINA) and O-acetyl tributyl citrate (ATBC). Dipropyl, dipentyl, dihexyl and dicyclohexyl phthalate were also analysed but not detected. The analytical procedure for this follow-up study was essentially the same as in the previous one. Detection limits were 0.1-15.6 ng g(-1) for each plasticizer. One-week duplicate diet samples provided by three hospitals in three remote prefectures of Japan were analysed as individual meals. DEHP was detected at 6-675 ng g(-1) in 62 of 63 meals, significantly lower levels compared with those detected in 1999. Levels of DEHA and DINP also decreased. The mean intake of plasticizers estimated from all samples was 160 microg DEHP day(-1), 12.5 microg DEHA day(-1), 4.7 microg DINP day(-1) and 3.4 microg BBP day(-1). Levels of DINA were relatively high in meals from one hospital: in those meals, the average daily intake was 1338 microg day(-1). Those of ATBC were also higher in meals from another hospital: the average daily intake was 1228 microg day(-1). The sources of DINA and ATBC can be cling-film or sausage packaging.
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Comparative Study |
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Tsumura Y, Yoshimura K, Tomaru N, Ohba K. Molecular phytogeny of conifers using RFLP analysis of PCR-amplified specific chloroplast genes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 91:1222-36. [PMID: 24170050 DOI: 10.1007/bf00220933] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/1995] [Accepted: 05/26/1995] [Indexed: 05/12/2023]
Abstract
We investigated the molecular phylogeny of conifers using restriction endonuclease fragment length polymorphism of six polymerase chain reaction-amplified chloroplast genes - frxC, rbcL, psbA, psbD, trnK, and 16S. We detected 227 total site changes among species, representing 23, 26, 38, 48, 67, and 25 site changes in frxC, psbA, psbD, rbcL, trnK and 16S, respectively. The mean nucleotide substitution was 10.75% (SD 0.573) among species in five families. Forty maximally parsimonious trees were obtained using the Wagner parsimony method, and a 50% majority-rule consensus tree was obtained from them. Data analysis produced similar basic patterns when both the Wagner parsimony and the neighbor-joining methods were applied, and the main lineages were clearly separated. Taxaceae and Cephalotaxaceae species were used as the out-groups when applying Wagner parsimony methods. With the Wagner method, the consistency index was 0.510, the retention index was 0.879, and tree length was 435 steps. Our results indicated that Cupressaceae and Taxodiaceae are closely related families and that Sciadopitys verticillata is the basal lineage of Cupressaceae and Taxodiaceae. The neighbor-joining tree is similar to the 50% majority-rule consensus of the 40 Wagner parsimony trees except for the position of Keteleeria daversifolia, the Picea and Cedrus group, and the divergence within Cupressaceae.
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Asuka Y, Tani N, Tsumura Y, Tomaru N. Development and characterization of microsatellite markers for Fagus crenata Blume. ACTA ACUST UNITED AC 2004. [DOI: 10.1046/j.1471-8286.2003.00583.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Shimono A, Ueno S, Gu S, Zhao X, Tsumura Y, Tang Y. Range shifts of Potentilla fruticosa on the Qinghai-Tibetan Plateau during glacial and interglacial periods revealed by chloroplast DNA sequence variation. Heredity (Edinb) 2009; 104:534-42. [DOI: 10.1038/hdy.2009.158] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Kitamoto N, Honjo M, Ueno S, Takenaka A, Tsumura Y, Washitani I, Ohsawa R. Spatial genetic structure among and within populations of Primula sieboldii growing beside separate streams. Mol Ecol 2005; 14:149-57. [PMID: 15643958 DOI: 10.1111/j.1365-294x.2004.02398.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigated the hierarchical genetic structure of SSR (simple sequence repeats) and cpDNA (chloroplast DNA) polymorphisms among and within populations of Primula sieboldii, a heterostylous clonal herb. Seven out of eight populations at the study site, located in a mountainous region of Nagano Prefecture, had each developed alongside a different stream, and the other occurred on a flat area 70 m from the nearest stream. The magnitude of genetic differentiation among streamside populations in maternally inherited cpDNA (Phi = 0.341) was much higher than that in biparentally inherited SSRs (Phi = 0.011). This result suggests that seed dispersal among streams was restricted, and pollen was the primary agent of gene flow among streamside populations. In contrast, genetic differentiation among subpopulations within streams were low at both markers (Phi = 0.053 for cpDNA, Phi = 0.025 for SSR). This low differentiation among subpopulations in cpDNA compared with that among streamside populations suggest that seed dispersal occur along the stream probably during flooding. This hypothesis was supported by the fact that in cpDNA haplotypes, no clear genetic structure was detected within the streamside population, while a significant genetic structure was found within 20 m in the nonstreamside population. Furthermore, within the streamside populations, two pairs of ramets with identical multilocus genotypes for eight SSR loci were distantly (> 50 m) distributed along the same streamside, suggesting dispersal of clonal propagule. Our study showed that the heterogeneity of the landscape can influence gene flow and hence spatial genetic structure.
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Research Support, Non-U.S. Gov't |
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Lee SL, Tani N, Ng KKS, Tsumura Y. Isolation and characterization of 20 microsatellite loci for an important tropical tree Shorea leprosula (Dipterocarpaceae) and their applicability to S. parvifolia. ACTA ACUST UNITED AC 2004. [DOI: 10.1111/j.1471-8286.2004.00623.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Suyama Y, Yoshimaru H, Tsumura Y. Molecular phylogenetic position of Japanese Abies (Pinaceae) based on chloroplast DNA sequences. Mol Phylogenet Evol 2000; 16:271-7. [PMID: 10942613 DOI: 10.1006/mpev.2000.0795] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The phylogenetic positions of Japanese Abies species (A. firma, A. homolepis, A. veitchii, A. sachalinensis, and A. mariesii) were revealed based on nucleotide sequences of chloroplast DNA. First, rbcL sequences of 24 Abies species worldwide were analyzed to clarify the phylogenetic position of the Japanese Abies within this genus. While 4 of the Japanese species formed a monophyletic group with almost no sequence divergence, A. mariesii was placed into a clearly different group with North American species. Second, to clarify the relationships among the species in the monophyletic group, sequences of rbcL, matK, and six spacer regions (total ca. 5 kb) were analyzed for 12 species of the group, with A. mariesii as an outgroup. Although a unique sequence and some species-specific sequences were detected in A. mariesii and in A. firma and A. homolepis, respectively, A. veitchii and A. sachalinensis gave identical sequences for all the sequenced regions.
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Asuka Y, Tomaru N, Munehara Y, Tani N, Tsumura Y, Yamamoto S. Half-sib family structure of Fagus crenata saplings in an old-growth beech-dwarf bamboo forest. Mol Ecol 2005; 14:2565-75. [PMID: 15969735 DOI: 10.1111/j.1365-294x.2005.02585.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Half-sib family structure of Fagus crenata saplings was examined in an old-growth beech-dwarf bamboo (Sasa spp.) forest using microsatellite genotypes in parentage analysis to identify the half-sib families in two 50 x 50 m plots: one with 36 adults, 641 saplings and no Sasa cover, the other with 21 adults, 61 saplings and Sasa cover. For large proportions of the saplings (44.6% and 75.4%, respectively) both of their parents were found within the same plot, indicating that pollination events frequently involved short-range pollen dispersal, probably because of the high density of adults in the study population. Although almost all of the adults had half-sib families, the number of offspring in the families was highly variable. In the plot with no Sasa cover, the variation in the number of offspring was significantly explained by the size of parents, i.e. the reproductive success is higher for large adults than for small adults. The half-sibs were aggregately distributed around their parents and the distribution overlapped among different half-sib families, which may be due to the limited seed dispersal and overlapping seed shadows of this species. As expected, there was weak genetic structure in the plot. By contrast, in the plot with Sasa cover, the half-sibs were distributed sparsely with a low density, and the degree of genetic structure was very weak. The difference in the half-sib family structure and genetic structure among saplings presumably reflects the difference in density that should be affected by regeneration dynamics associated with environmental conditions.
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Research Support, Non-U.S. Gov't |
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Yoshii K, Kaihara A, Tsumura Y, Ishimitsu S, Tonogai Y. Liquid chromatographic determination of emamectin, milbemectin, ivermectin and abamectin in crops and confirmation by liquid chromatography-mass spectrometry. J Chromatogr A 2000; 896:75-85. [PMID: 11093642 DOI: 10.1016/s0021-9673(00)00466-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Emamectin, milbemectin, ivermectin and abamectin are similar macrocyclic lactone chemicals used as an acaricides or parasiticides. We developed a simultaneous analytical method for determining the residual amounts of these compounds and emamectin metabolites in crops. A sample extracted with acetone was cleaned up with Bond Elut C18 and NH2. The sample was then fluorescence-derivatized with trifluoroacetic anhydride and 1-methylimidazole in acetonitrile. The analyte was measured by HPLC with fluorescence detection using an octadecylsilyl column with 3 microm particle size and gradient elution. In most crops, their recoveries by the developed method were ca. 80-110%. The detection limits of the analytes in vegetables were 0.1-0.3 ppt. Using the developed method, we surveyed the residues of these compounds in 20 commercial crops in Osaka, Japan. The result of the surveillance was that emamectin benzoate of 0.2-6.7 ppb was detected in nine cases and milbemectin of 16.7-279.3 ppb was detected in four cases. The detected samples were confirmed by LC-electrospray ionization (ESI) MS. The limit of detection by LC-ESI-MS was similar to the fluorescence detection level of 0.1-0.3 ppt in vegetables except for milbemectin.
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Torimaru T, Tani N, Tsumura Y, Nishimura N, Tomaru N. EFFECTS OF KIN-STRUCTURED SEED DISPERSAL ON THE GENETIC STRUCTURE OF THE CLONAL DIOECIOUS SHRUB ILEX LEUCOCLADA. Evolution 2007; 61:1289-300. [PMID: 17542840 DOI: 10.1111/j.1558-5646.2007.00108.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nonrandom patterns of gene dispersal have been identified as possible causes of genetic structuring within populations. Attempts to model these patterns have generally focused solely on the effects of isolation by distance, but the processes involved are more complex than such modeling suggests. Here, we extend considerations of gene dispersal processes beyond simple isolation by distance effects by directly evaluating the effects of kin-structured gene dispersal mediated by the group dispersal of related seeds within fruits (i.e., kin-structured seed dispersal) by birds on genetic structure in Ilex leucoclada, a clonal dioecious shrub. To examine the genetic structure patterns, we established two 30x30 m plots (one with immature soils in old-growth forest and one in secondary forest, designated IM and SC, respectively) with different I. leucoclada stem densities. In these two plots 145 and 510 stems were found, representing 78 and 85 genets, respectively, identified by analyzing their genotypes at eight microsatellite loci. The clonal structure was stronger in the SC plot than in the IM plot. Correlograms of coancestry for genets in both plots exhibited significant, positive, high values in the shortest distance class, indicating the presence of strong genetic structure. However, Sp statistics revealed that the pattern of the genetic structure differed between the plots. In addition, to estimate the family structure within fruits, we sampled forty fruits, in total, from 15 randomly selected plants in the area around the IM and SC plots, and found that 80% of the fruits were multiseeded and 42-100% of the multiseeded fruits contained at least one pair of full sibs. Simulations based on these estimates demonstrated that the group dispersal of related seeds produced through correlated mating both within and across fruits, but not unstructured half-sib dispersal, could generate the observed magnitude and trends of genetic structure found in the IM plot. Furthermore, in addition to kin-structured seed dispersal, isolation by distance processes is also likely to promote genetic substructuring in the SC plot. After discussing possible ecological factors that may have contributed to the observed genetic structure, we contrast our results with those predicted by general isolation by distance models, and propose that kin-structured seed dispersal should promote some evolutionary phenomena, and thus should be incorporated, where appropriate, in models of gene dispersal in natural plant populations.
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Okamura K, Kinukawa T, Tsumura Y, Otani T, Itoh H, Kobayashi H, Matsuura O, Kobayashi M, Fukatsu T, Ohshima S. A randomized study of short-versus long-term intravesical epirubicin instillation for superficial bladder cancer. Nagoya University Urological Oncology Group. Eur Urol 2000; 33:285-8; discussion 289. [PMID: 9555553 DOI: 10.1159/000019581] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
OBJECTIVE A prospective randomized study was undertaken to determine whether prophylactic maintenance instillation of epirubicin following induction treatment is beneficial in patients with superficial bladder cancer. PATIENTS AND METHODS One hundred and forty-eight patients with resectable superficial bladder cancer (Ta-1, single, multiple, primary or recurrent with, however, no recurrence during the last year) were enrolled in this study. In both arms, epirubicin (40 mg/ml in normal saline) was administered six times within 4 weeks after a transurethral resection of the bladder tumor(s). In arm A, the patients received 11 additional monthly instillations of epirubicin. RESULTS Of the 148 patients, 138 (93.2%) were eligible and followed for an average of 29.6 months. 93 (67.4%) had a solitary tumor. No significant difference in the recurrence-free curve was observed between the two arms (p = 0.62). The recurrence rate per year was 0.16 in arm A and 0.17 in arm B. Toxicity included vesical irritability in 10 (7.2%) and hematuria in 1 patient. No significant difference in the frequency or degree of toxicity was observed between the two arms. CONCLUSION These data suggest that maintenance instillation of epirubicin does not reduce superficial bladder cancer recurrence.
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Kusumi J, Tsumura Y, Yoshimaru H, Tachida H. Phylogenetic relationships in Taxodiaceae and Cupressaceae sensu stricto based on matK gene, chlL gene, trnL-trnF IGS region, and trnL intron sequences. AMERICAN JOURNAL OF BOTANY 2000; 87:1480-1488. [PMID: 11034923 DOI: 10.2307/2656874] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nucleotide sequences from four chloroplast genes, the matK, chlL, intergenic spacer (IGS) region between trnL and trnF, and an intron of trnL, were determined from all species of Taxodiaceae and five species of Cupressaceae sensu stricto (s.s.). Phylogenetic trees were constructed using the maximum parsimony and the neighbor-joining methods with Cunninghamia as an outgroup. These analyses provided greater resolution of relationships among genera and higher bootstrap supports for clades compared to previous analyses. Results indicate that Taiwania diverged first, and then Athrotaxis diverged from the remaining genera. Metasequoia, Sequoia, and Sequoiadendron form a clade. Taxodium and Glyptostrobus form a clade, which is the sister to Cryptomeria. Cupressaceae s.s. are derived from within Taxodiaceae, being the most closely related to the Cryptomeria/Taxodium/Glyptostrobus clade. These relationships are consistent with previous morphological groupings and the analyses of molecular data. In addition, we found acceleration of evolutionary rates in Cupressaceae s.s. Possible causes for the acceleration are discussed.
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Tsumura Y, Suyama Y, Yoshimura K. Chloroplast DNA inversion polymorphism in populations of Abies and Tsuga. Mol Biol Evol 2000; 17:1302-12. [PMID: 10958847 DOI: 10.1093/oxfordjournals.molbev.a026414] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Polymorphism for a 42-kb chloroplast DNA inversion was detected in five species of Abies and two species of Tsuga based on a sample of 1,281 individuals and both Southern hybridization and polymerase chain reaction (PCR) analyses. Two haplotypes were observed in all populations and species. The 42-kb inversion is associated with a short inverted repeat that includes trnS, psaM, and trnG. The frequencies of the two haplotypes within species were very similar among the five species of Abies This polymorphism has been maintained within populations and species in both Abies and Tsuga, probably because the mutation rate of the inversion is high. Haplotype frequencies had no geographical tendencies for any species except Abies mariesii, in which haplotype frequencies varied clinally, possibly as a result of rapid dissemination after the most recent glacial period and random genetic drift.
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MESH Headings
- Blotting, Southern
- Chromosome Inversion
- Cycadopsida/genetics
- DNA, Chloroplast/chemistry
- DNA, Chloroplast/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- Gene Frequency
- Genetic Variation
- Genetics, Population
- Haplotypes
- Japan
- Molecular Sequence Data
- Polymerase Chain Reaction
- Polymorphism, Genetic
- Polymorphism, Restriction Fragment Length
- Repetitive Sequences, Nucleic Acid
- Sequence Analysis, DNA
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Nakamura Y, Tsumura Y, Tonogai Y, Shibata T. Fecal steroid excretion is increased in rats by oral administration of gymnemic acids contained in Gymnema sylvestre leaves. J Nutr 1999; 129:1214-22. [PMID: 10356090 DOI: 10.1093/jn/129.6.1214] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Gymnemic acids are the saponins with a triterpenoid structure contained in Gymnema sylvestre leaves and have the hypoglycemic effects. In spite of the cholesterol-binding properties of saponins, the effect of gymnemic acids on cholesterol metabolism has not been elucidated to date. We investigated the effects of gymnemic acids on fecal steroid excretion in rats. Three kinds of extracts from Gymnema sylvestre leaves, extract (GSE), acid precipitate (GSA) and column fractionate (GSF), of which the gymnemagenin (an aglycone of gymnemic acids) concentrations are 58.87, 161.6, and 363.3 mg/g respectively, were used for the experiments. These were administered to rats orally at the dose of 0.05-1.0 g/kg for 22 d. Rats were given free access to water and nonpurified diet without cholesterol, and the differences in fecal excretion of steroids and gymnemic acids were investigated. Although there were no significant effects of GSE, GSA and GSF decreased body weight gain and food intakes in a dose-dependent manner (P < 0.01). GSF (1.0 g/kg) significantly increased fecal excretion of neutral steroids and bile acids in a dose-dependent manner (P < 0.05), especially those of cholesterol and cholic acid (CA)-derived bile acids. The increases in fecal steroid excretion of cholesterol, total neutral steroids, total bile acids and CA-related bile acids were acute and significantly correlated with fecal gymnemagenin levels (r2 = 0.2316-0.9861, P < 0. 05). These results demonstrated for the first time that a high dose of gymnemic acids increases fecal cholesterol and CA-derived bile acid excretion. Further studies are needed to clarify the effect of gymnemic acids on cholesterol metabolism.
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