Biomedical subjects

Nam-Soo Kim

Publications and source records attributed to Nam-Soo Kim.

18 recordsLinked to original sources

PubMed2006

Mechanisms underlying TGF-beta1-induced expression of VEGF and Flk-1 in mouse macrophages and their implications for angiogenesis.

TGF-beta induces vascular endothelial growth factor (VEGF), a potent angiogenic factor, at the transcriptional and protein levels in mouse macrophages. VEGF secretion in response to TGF-beta1 is enhanced by hypoxia and by overexpression of Smad3/4 and hypoxia-inducible factor-1alpha/beta (HIF-1alpha/beta). To examine the transcriptional regulation of VEGF by TGF-beta1, we constructed mouse reporters driven by the VEGF promoter. Overexpression of HIF-1alpha/beta or Smad3/4 caused a slight increase of VEGF promoter activity in the presence of TGF-beta1, whereas cotransfection of HIF-1alpha/beta and Smad3/4 had a marked effect. Smad2 was without effect on this promoter activity, whereas Smad7 markedly reduced it. Analysis of mutant promoters revealed that the one putative HIF-1 and two Smad-binding elements were critical for TGF-beta1-induced VEGF promoter activity. The relevance of these elements was confirmed by chromatin immunoprecipitation assay. p300, which has histone acetyltransferase activity, augmented transcriptional activity in response to HIF-1alpha/beta and Smad3/4, and E1A, an inhibitor of p300, inhibited it. TGF-beta1 also increased the expression of fetal liver kinase-1 (Flk-1), a major VEGF receptor, and TGF-beta1 and VEGF stimulated pro-matrix metalloproteinase 9 (MMP-9) and active-MMP-9 expression, respectively. The results from the present study indicate that TGF-beta1 can activate mouse macrophages to express angiogenic mediators such as VEGF, MMP-9, and Flk-1.

Animals↗

PubMed2006

Ketamine-induced cardiac depression is associated with increase in [Mg2+]i and activation of p38 MAP kinase and ERK 1/2 in guinea pig.

This study investigated the signaling pathways responsible for ketamine-induced cardiac depression in guinea pigs. The left ventricular development pressure (LVDP), velocity of the change in pressure (dP/dt), and heart rate (HR) accompanied with the total magnesium efflux ([Mg]e) were measured simultaneously in perfused hearts. The level of activation of the extracellular signal-regulated kinases 1/2 (ERK 1/2) and p38 mitogen-activated protein (MAP) kinase. The intracellular ionized magnesium concentration ([Mg2+]i) was measured using Mag-fura 2 AM in a single cardiomyocyte. Ketamine produced reversible decreases in the LVDP, dP/dt, and HR accompanied by increases in the [Mg]e. Ketamine also produced significant activation of p38 MAP kinase and ERK 1/2, and produced a dose-dependent increase in the [Mg2+]i, which was inhibited SB203580 and PD98059. These results suggest that ketamine-induced cardiac depression can be partly responsible for the increase in [Mg2+]i and [Mg]e, accompanied by the activation of p38 MAP kinase and ERK 1/2 in guinea pigs.

Animals↗

PubMed2006

CACTA and MITE transposon distributions on a genetic map of rice using F15 RILs derived from Milyang 23 and Gihobyeo hybrids.

Up to 35% of the rice genome consists of various kinds of transposons, and CACTA and MITE are two of the major class 2 DNA transposons in the genome. We have employed the consensus sequences of Rim2/Hipa CACTA, Stowaway MITE Pangrangja, and Tourist MITE Ditto for transposon display (TD) analysis to locate them on a genetic map, with 58 SSR markers used to anchor them. The TD analysis produced a high profile of the polymorphisms between the parental lines, Oryza sativa var. Gihobyeo/O. sativa var. Milyang, in intraspecific F15 RIL lines, locating 368 markers of Rim2/Hipa CACTA, 78 markers of Tourist MITE Ditto, and 22 markers of Stowaway MITE Pangrangja. In the segregation analysis, non-parental segregating bands and segregation distortion bands were observed. The recombinant genetic map spans 3023.9 cM, with 5.7 cM the average distance between markers. The TD markers were distributed unequally on the chromosomes because many TD markers were located in pericentric chromosomal regions except in the cases of chromosomes 2, 3, 6 and 9. Although the number of transposon markers was not sufficient to include all rice class 2 transposons, the current map of CACTA and MITE transposons should provide new insight into the genome organization of rice since no previous DNA transposon map is available.

Chromosome Mapping↗

PubMed2006

Genetic mapping of the Isaac-CACTA transposon in maize.

We constructed a genetic linkage map with Isaac-TD, SSR, and SNAP markers in a RIL population which had been derived from a cross of waxy corn (KW7) and dent corn (Mo17). A total of 368 markers, including 241 Isaac-TD, 121 SSR, and 6 SNAP markers, were assigned to 10 linkage groups, encompassing 1687.0 cM, with an average genetic distance of 4.6 cM between markers. SSR markers were utilized as chromosome anchors, in order to assign the Isaac-TD markers to the chromosomes, and the number of markers in each of the linkage groups ranged between 22 and 49. The majority of the Isaac-TD markers were determined to have been distributed throughout the ten maize chromosomes. In linkage analysis of the Isaac-TD markers with genes of agronomic interest, six genes related with maize kernel starch biosynthesis, ae1, bt2, sh1, sh2, su1, and wx1, were analyzed and shown that they were closely linked with either the Isaac-TD or SSR markers on chromosomes of 3, 4, 5, and 9. We observed and mapped segregation-distorted markers on chromosomes 1, 5, 6, 7, 8, and 10, where these markers were clustered. The Isaac-TD or SSR markers which were closely linked with starch synthesis genes may prove useful in marker-assisted breeding programs.

Base Sequence↗

PubMed2006

Immunosuppressants inhibit hormone-stimulated Mg2+ uptake in mouse distal convoluted tubule cells.

Immunosuppressants such as cyclosporinA and FK506 (tacrolimus) are widely prescribed to treat numerous disorders and to treat organ transplant recipients. However, cyclosporine A and FK506 are both known to produce hypomagnesaemia. The mechanism of this effect is still unclear. The present study determined the effects of immunosuppressant treatment on the parathyroid hormone (PTH) mediated Mg(2+) uptake and the mitogen-activated protein kinase (MAPK) activation in mouse distal convoluted tubule (MDCT) cells. The intracellular Ca(2+) and Mg(2+) concentrations in a single MDCT cell were measured by using the fluorescentdye Fura-2 AM and Mag-fura-2 AM, respectively. Cyclosporine A and FK506 illicited a transient increase of intracellular Ca(2+) from a basal level of 99 +/- 16 nM to 685 +/- 105 and 608 +/- 96 nM, respectively. In order to determine the Mg(2+) transport, the MDCT cells were Mg(2+)-depleted by culturing them in Mg(2+)-free media for 16 h, and the Mg(2+) uptake was measured by microfluorescence after placing the depleted cells in 1.5mM MgCl(2). The mean rate of Mg(2+) uptake, d([Mg(2+)](i))/dt, was 140 +/- 16 nM/s in the control MDCT cells. PTH increased the Mg(2+) uptake more than 2 times in this cell. Cyclosporine A (10 microM) and FK506 (0.1 microM) did not affect the basal Mg(2+)uptake (140 +/- 16 and 142 +/- 14 nM/s, respectively), but they inhibited the PTH-stimulated Mg(2+) entry, decreasing it from 248+/-12 to 147 +/- 7 and 148 +/- 14 nM/s, respectively. These effects were inhibited by L685818, which is a potent competitive antagonist of FK506. PTH stimulated the extracellular signal-regulated kinase1/2 (ERK1/2) protein synthesis. This PTH-stimulated ERK1/2 activation was inhibited by cyclosporine A and FK506. In the present study, the role of ERK1/2 activation on the PTH-dependent magnesium uptake was examined in MDCT cells, and we showed that immunosuppressants inhibit the hormone-stimulated Mg(2+) uptake into the MDCT cells by inhibiting the MAPK pathway.

Animals↗

PubMed2006

Genetic diversity of maize kernel starch-synthesis genes with SNAPs.

Measuring genetic diversity in populations of a crop species is very important for understanding the genetic structure of and subsequently improving the crop species by genetic manipulation. Single-nucleotide amplified polymorphisms (SNAPs) among and within maize populations of waxy, dent, and sweet corns at 25 single-nucleotide polymorphism (SNP) sites in 6 kernel starch-synthesis genes (sh2, bt2, su1, ae1, wx1, and sh1) were determined. Because of the intensive selection of some favorable alleles in starch-synthesis genes during the breeding process, and the resultant strong linkage disequilibrium (LD), the number of haplotypes in each population was far less than expected. Subsequent phenetic clustering analysis with the SNAPs indicated that the dent, waxy, and sweet corns formed distinct subclusters, except in a few incidences. LD was surveyed among SNAPs of intragenic, intergenic, and intrachromosomal SNPs in whole and subpopulations, which revealed that some SNAPs showed high LD with many other SNAPs, but some SNAPs showed low or no significant LD with others, depending on the subpopulation, indicating that these starch genes have undergone different selection in each subpopulation during the breeding process. Because the starch synthesis genes used in this study are important in maize breeding, the genetic diversity, LD, and accessions having rare SNAP alleles might be valuable in maize improvement programs.

Alleles↗

PubMed2006

Genetic diversity and phylogenetic relationship in AA Oryza species as revealed by Rim2/Hipa CACTA transposon display.

CACTA is a class 2 transposon, that is very abundantly present in plant genomes. Using Rim2/Hipa CACTA transposon display (hereafter Rim2/Hipa-TD), we analyzed several A-genome diploid Oryza species that have a high distribution of the CACTA motifs. High levels of polymorphism were detected within and between the Oryza species. The African taxa, O. glaberrima and O. barthii, both showed lower levels of polymorphism than the Asian taxa, O. sativa, O. rufipogon, and O. nivara. However, O. longistaminata, another African taxon, showed levels of polymorphism that were similar to the Asian taxa. The Latin American taxon, O. glumaepatula, and the Australian taxon, O. meridionalis, exhibited intermediate levels of polymorphism between those of the Asian and African taxa. The lowest level of polymorphism was observed in O. glaberrima (32.1%) and the highest level of polymorphism was observed in O. rufipogon (95.7%). The phylogenetic tree revealed three major groups at the genetic similarity level of 0.409. The first group consisted of three Asian taxa, O. sativa, O. rufipogon and O. nivara. The second group consisted of three African taxa, O. glaberrima, O. barthii, O. longistaminata, and an American taxon, O. glumaepatula. The third group contained an Australian taxon, O. meridionalis. The clustering patterns of these species matched well with their geographical origins. Rim2/Hipa-TD appears to be a useful marker system for studying the genetic diversity and species relationships among the AA diploid Oryza species.

Chromosome Mapping↗

PubMed2006

Distribution of cortical bone in bovine limbs.

Xenogenic bone grafts have been widely researched because they are not limited in terms of volume and size like autogenous and allogenic grafts, and the favored bone for xenografts is bovine bone. However, the efficacy of cortical bone from bovine limb for xenografts is not clearly known. In this study, the distribution of cortical bone in bovine humerus, radius, femur, and tibia were investigated. Each experimental bone was split longitudinally with a bone saw and bone marrow and cancellous bone were removed. The thicknesses of cortical layers in sample diaphyses were measured at 1cm intervals using a micrometer. The mean lengths of cortical portions were; humerus 14.7 +/- 2.3 cm, radius 19.0 +/- 2.6 cm, femur 19.0 +/- 3.2 cm, and tibia 23.0 +/- 3.1 cm. Thickest cortical bone was found at the distal caudal metaphysis of the humerus, the proximal caudal metaphysis of the radius, the craniolateral and caudomedial midshaft of the femur and the lateral and medial midshaft of tibia. The mean surface areas of cortical bone were humerus 187.4 +/- 15.44 cm2, radius 229.2 +/- 43.31 cm2, femur 295.8 +/- 8.93 cm2, and tibia 290.0 +/- 30.44 cm2. And, mean volumes of cortical bone were humerus 149.42 +/- 15.35 cm3, radius 166.26 +/- 20.02 cm3, in femur 220.45 +/- 22.73 cm3, and tibia 214.89 +/- 20.05 cm3. The results of this study can be used to produce cortical bone-based plates and screws.

Animals↗

PubMed2005

Evaluation of silymarin in the treatment on asymptomatic Giardia infections in dogs.

We have reported previously the efficacy of antiprotozoal drugs against canine giardiasis (In press, Journal of Veterinary Clinic, the Korean Society of Veterinary Clinics). Fenbendazole was found to be the most efficacious for the treatment of canine giardiasis. There were no significant differences between the efficacy of albendazole and fenbendazole against canine giardiasis. On the other hand, the efficacy of metronidazole for the treatment of canine giardiasis, the efficacy was lower when compared to that of albendazole and fenbendazole. On the basis of these results, to evaluate clinical effect of silymarin, we evaluated the therapeutic efficacy of metronidazole alone, or combined with silymarin for 2 weeks for canine giardiasis. In addition, to observe effects on nutrition, we investigated the changes of body weight, the serum biochemical indicators for liver inflammation (GOT, GPT, NH3), the liver cell regeneration indicators (total protein, albumin) and the hematological changes during treatment (WBC, RBC, MCV, MCH and MCHC). The dogs were allocated to four groups; one group was treated with silymarin (3.5 mg/kg once a day, oral), another with metronidazole (50 mg/kg once a day, oral), and the other group with silymarin (3.5 mg/kg once a day, oral) plus metronidazole (50 mg/kg once a day, oral), while control group remained nontreated. The fecal samples from all the dogs were examined, using the ZSCT and giardia antigen test kit (SNAP(*) Giardia, IDEXX Laboratories), from each dog of each group for three times a week for 2 weeks. Dogs were considered to have giardiasis when one or more of the fecal samples had positive results for Giardia cysts. Seven days after treatment, the efficacy of silymarin plus metronidazole was found 79%, whereas that of metronidazole was 72%. Ten days post-treatment the efficacy of metronidazole plus silymarin (91%) was significantly different in comparison with that of metronidazole (75%). Two weeks post-treatment no cysts were detected in the fecal samples in the dogs of metronidazole or silymarin plus metronidazole-treated groups. Whereas, the fecal samples of all the dogs of the control and only silymarin-treated groups were giardia positive. Signs of side effects were not observed in silymarin plus metronidazole-treated dogs. But poor appetite and intermittent vomiting signs were observed in two dogs of the metronidazole-treated group that resolved when metronidazole administration was discontinued. The body weight of those treated with metronidazole was significantly decreased in comparison with those treated with silymarin and metronidazole plus silymarin. There were significant differences of body weight between the dogs treated with silymarin and metronidazole. Two weeks after metronidazole treatment, serum concentration of GOT, GPT and NH3 were significantly increased in comparison with those treated with silymarin. On the other hand, the serum concentration of GOT, GPT and NH3 were not significantly increased when treated with silymarin plus metronidazole compared to those treated with metronidazole. Serum total protein and albumin concentrations were decreased after metronidazole treatment as compared to those treated with silymarin and silymarin plus metronidazole. The concentrations of serum total protein and albumin decreased significantly in metronidazole-treated group as compared to that of treated with silymarin. The numbers of WBC and RBC did show significant differences in the dogs treated with metronidazole, while MCV, MCH were significant by different between silymarin and metronidazole-treated dogs. On the other hand, there were no significant differences in MCHC in any groups. These data suggest that silymarin, in supplement with antiprotozoal drugs, can influence the therapy of canine giardiasis.

Administration, Oral↗

PubMed2005

alpha(1)-Agonists-induced Mg(2+) efflux is related to MAP kinase activation in the heart.

The stimulation of the alpha(1)-adrenergic receptor with phenylephrine results in the significant extrusion of Mg(2+) from the rat heart and cardiomyocytes. Phenylephrine-induced Mg(2+) extrusion is prevented by the removal of extracellular Ca(2+) or by the presence of Ca(2+)-channel blockers such as verapamil, nifedipine, or (+)BAY-K8644. Mg(2+) extrusion is almost completely inhibited by PD98059 (a MAP kinase inhibitor). The simultaneous addition of 5mM Ca(2+) and phenylephrine increases the extrusion of Mg(2+) from perfused hearts and cardiomyocytes. This Mg(2+) extrusion is inhibited by more than 90% when the hearts are preincubated with PD98059. ERKs are activated by perfusion with either phenylephrine or 5mM Ca(2+). This ERK activation is inhibited by PD98059. Overall, these results suggest that stimulating the cardiac alpha(1)-adrenergic receptor by phenylephrine causes the extrusion of Mg(2+) via the Ca(2+)-activated, Na(+)-dependent transport pathway, and the ERKs assists in Mg(2+) transport in the heart.

Adrenergic alpha-1 Receptor Agonists↗

PubMed2005

Rim 2/Hipa CACTA transposon display: a new genetic marker technique in Oryza species.

BACKGROUND: Transposons constitute the major fractions of repetitive sequences in eukaryotes, and have been crucial in the shaping of current genomes. Transposons are generally divided into two classes according to the mechanism underlying their transposition: RNA intermediate class 1 and DNA intermediate class 2. CACTA is a class 2 transposon superfamily, which is found exclusively in plants. As some transposons, including the CACTA superfamily, are highly abundant in plant species, and their nucleotide sequences are highly conserved within a family, they can be utilized as genetic markers, using a slightly modified version of the conventional AFLP protocol. Rim2 /Hipa is a CACTA transposon family having 16 bp consensus TIR sequences to be present in high copy numbers in rice genome. This research was carried out in order to develop a Rim2/Hipa CACTA-AFLP or Rim2/Hipa CACTA-TD (transposon display, hereafter Rim2/Hipa-TD) protocol for the study of genetic markers in map construction and the study of genetic diversity in rice. RESULTS: Rim2/Hipa-TD generated ample polymorphic profiles among the different rice accessions, and the amplification profiles were highly reproducible between different thermocyclers and Taq polymerases. These amplification profiles allowed for clear distinction between two different ecotypes, Japonica and Indica, of Oryza sativa. In the analysis of RIL populations, the Rim2/Hipa-TD markers were found to be segregated largely in a dominant manner, although in a few cases, non-parental bands were observed in the segregating populations. Upon linkage analysis, the Rim2/Hipa-TD markers were found to be distributed in the regions proximal to the centromeres of the chromosomes. The distribution of the Rim2/Hipa CACTA elements was surveyed in 15 different Oryza species via Rim2/Hipa-TD. While Rim2/Hipa-TD yielded ample amplification profiles between 100 to 700 bp in the AA diploid Oryza species, other species having BB, CC, EE, BBCC and CCDD, profiles demonstrated that most of the amplified fragments were larger than 400 bp, and that our methods were insufficient to clearly distinguish between these fragments. However, the overall amplification profiles between species in the Oryza genus were fully distinct. Phenetic relationships among the AA diploid Oryza species, as evidenced by the Rim2/Hipa-TD markers, were matched with their geographical distributions. CONCLUSION: The abundance of the Rim2/Hipa TIR sequences is very informative since the Rim2/Hipa-TD produced high polymorphic profiles with ample reproducibility within a species as well as between species in the Oryza genus. Therefore, Rim2/Hipa-TD markers can be useful in the development of high-density of genetic map around the centromeric regions. Rim2/Hipa-TD may also prove useful in evaluations of genetic variation and species relationships in the Oryza species.

Base Sequence↗

PubMed2005

Isaac-CACTA transposons: new genetic markers in maize and sorghum.

CACTA is an En/Spm transposon superfamily present in high copy number in plant genomes, and Isaac is a subfamily of the CACTA superfamily. The TIR sequence of the Isaac subfamily was used for the purpose of transposon display (TD) in maize and sorghum. The Isaac TD produced 50-80 amplified fragments, depending on the primer combination, and the amplification profile was highly polymorphic among maize inbred lines. Isaac TD-based phylogenetic clustering distinguished the maize inbred lines according to their lineages and was consistent with the results of phylogenetic reports derived from other marker techniques by others researchers. The Isaac TD profile proved to be highly reproducible with different brands of Taq DNA polymerases and thermocyclers. The Isaac TD was also applied to recombinant inbred lines to assess genetic segregation; we observed 40-50 recordable segregation markers, depending on the primer combination. These Isaac TD markers segregated mostly as dominant markers, although, in a few cases, non-parental bands were observed in the segregating populations. In addition, the Isaac TD was very successful in the amplification of sorghum accessions. Therefore, the Isaac TD may provide another useful protocol for genetic analysis in maize and sorghum.

DNA Primers↗

PubMed2005

Trochleoplasty in lateral patellar luxation in two calves.

Two Holstein Friesian calves were referred to the Animal Medical Center of Chonbuk National University with severe lameness on the hind limb(s), flexed stifle joint and an inability to walk since birth. Based on the clinical history, clinical findings and radiography of the stifle joint, the cases were diagnosed as grade III lateral patellar luxation (LPL). Trochleoplasty along with medial retinacular reinforcement and lateral release were performed in both calves. The calves recovered 3 to 4 weeks after surgery. Trochleoplasty along with medial retinacular reinforcement and lateral release can be an effective technique for the treatment of LPL in calves.

Animals↗

PubMed2005

Total hip replacement in a dog.

An intact male German shepherd dog (4 y, body wt. 35.5 kg) was referred to the Animal Medical Center, Chonbuk National University with severe lameness, pain and gait abnormality on the right hind limb. Survey radiographs of the pelvis revealed dysplasia of the right coxofemoral joint with subluxation. The dog was surgically treated performing total hip replacement (THR) using Modular Biolox Canine Modular THR System. The dog began to bear weight and slowly returned to a normal exercise pattern 2 months after surgery. THR resulted in satisfactory clinical functions with 6 months follow up and no complications were observed. Canine modular THR could be a successful modality for the management of disabling conditions of the coxofemoral joint.

Animals↗

PubMed2004

Isolation of callus-specific mRNAs from differentiating embryogenic somatic calli of Pimpinella brachycarpa by cDNA-AFLP.

We used cDNA-AFLP to analyze gene expression profiles during somatic embryogenesis and to isolate stage-specific genes in Pimpinella brachycarpa. Ninety-six combinations of AFLP primers produced 3,785 fragments, of which 478, 403, and 436 were specific to calli, somatic embryos, and plants, respectively. 262 fragments were shared by callus and somatic embryo, 324 by somatic embryo and plant, and 222 by callus and plant. The number of fragments common to all three stages was 1,660. Seventy-five of the 478 callus-specific fragments were cloned and sequenced and their functions sought in the GenBank database. Thirty-three of them showed significant homology to GenBank data base entries and twelve of these were homologous to genes with products of known function such as ATPases, tubulins, kinases, transcription factors, ubiquitins, and ankyrin. Callus-specific expression was confirmed by performing RT-PCR with six of the twelve fragments. Since the somatic embryo is induced by auxin (Thidiazuron), possible down regulation of these genes by auxin is also discussed.

Adenosine Triphosphatases↗

PubMed2004

Synthesis and cytotoxic activity of 1-(1-benzoylindoline-5-sulfonyl)-4-phenylimidazolidinones.

The novel 1-(1-benzoylindoline-5-sulfonyl)-4-phenyl-4,5-dihydroimidazolones 2 shows highly potent and broad cytotoxicities. Their cytotoxicities against human lung carcinoma A549, human chronic myelogenous leukemia K562, and human ovarian adenocarcinoma SK-OV-3 are compatible with doxorubicin. Compound 2p (1-[(4-aminobenzoyl)indoline-5-sulfonyl])-4-phenyl-4,5-dihydroimidazolone) exhibits a cytotoxicity that is far more potent than doxorubicin and also exhibits highly effective antitumour activities against murine (3LL, Colon 26) and human xenograft (NCI-H23, SW620) tumor models.

Animals↗

PubMed2003

A new MITE family, Pangrangja, in Gramineae species.

The miniature inverted-repeat transposable element (MITE) is a type of class II transposon. We have isolated a new MITE, Pangrangja, from the species Oryza. Although Pangrangja elements are present in a number of Gramineae species, they are more prevalent in A genome Oryza species, Triticum, Aegilops, Hordeum, and Tripsacum. The Pangrangja has a 16 bp terminal inverted repeat (TIR) and conserved trinucleotides 5'-TTG-3' and 5'-AAA-3' at both ends. The TIR starts with 5'-CAGT-3', similar to the MITEs of the Emigrant family. The sequences between TIRs are very AT-rich and vary in length from 161 bp in A genome Oryza species to 513 bp in Hordeum vulgare. While the size and sequence of Pangrangia elements are conserved in the A genome Oryza species, there is some sequence variation in other plants. In an analysis of the mobile history of Oryza sativa, eight RESites (related to empty sites) were found and grouped into three types depending on the presence or absence of the conserved trinucleotides 5'-TTG-3' and 5'-AAA-3'. Since one of the RESites showed a perfect palindromic 22 bp sequence into which 180 bp of the Pangrangja element was inserted, the possible role of secondary structure of the palindromic sequences is discussed. We also suggest that as Pangrangja MITE-AFLP has been successful in many different Gramineae, Pangrangja elements may be useful in the genomic analysis of grasses.

Base Sequence↗

PubMed2003

Genetic variation in Oryza species detected by MITE-AFLP.

MITE-AFLP markers were successfully used to study the genetic variation and species relationship in Oryza species. Analysis of 53 accessions of Oryza species with seven MITE-AFLP primer combinations detected a total of 250 polymorphic fragments. High polymorphism was detected within and between Oryza species. Species relationships were analyzed by the pattern of presence or absence of homologous fragments, because nucleotide sequences of the detected MITE-AFLP fragments revealed that the same fragments in different species shared very high sequence homology. The genetic distances (GDs) between species were higher than those within species and the GDs in O. sativa complex were higher than those in O. officinalis complex. The phylogenetic tree recognized two major groups at 62% genetic similarity; group I consists of all AA genome species of the O. sativa complex, and group II consists of BB-, CC-, EE- and BBCC genome species of the O. officinalis complex. Therefore, this study demonstrated that the MITE-AFLP technique provide a tool for studying the genetic variation and species relationship in Oryza species.

DNA Transposable Elements↗