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

DNA microarrays on a dendron-modified surface improve significantly the detection of single nucleotide variations in the p53 gene

Selectivity and sensitivity in the detection of single nucleotide polymorphisms (SNPs) are among most important attributes to determine the performance of DNA microarrays. We previously reported the generation of a novel mesospaced surface prepared by applying dendron molecules on the solid surface. DNA microarrays that were fabricated on the dendron-modified surface exhibited outstanding performance for the detection of single nucleotide variation in the synthetic oligonucleotide DNA. DNA microarrays on the dendron-modified surface were subjected to the detection of single nucleotide variations in the exons 5–8 of the p53 gene in genomic DNAs from cancer cell lines. DNA microarrays on the dendron-modified surface clearly discriminated single nucleotide variations in hotspot codons with high selectivity and sensitivity. The ratio between the fluorescence intensity of perfectly matched duplexes and that of single nucleotide mismatched duplexes was >5–100 without sacrificing signal intensity. Our results showed that the outstanding performance of DNA microarrays fabricated on the dendron-modified surface is strongly related to novel properties of the dendron molecule, which has the conical structure allowing mesospacing between the capture probes. Our microarrays on the dendron-modified surface can reduce the steric hindrance not only between the solid surface and target DNA, but also among immobilized capture probes enabling the hybridization process on the surface to be very effective. Our DNA microarrays on the dendron-modified surface could be applied to various analyses that require accurate detection of SNPs

Atypical iliac vein compression in patients with symptomatic May–Thurner syndrome

PURPOSEWe aimed to investigate the incidence, etiology, treatment, and clinical course of atypical iliac vein compressions (AIVCs) among patients with May–Thurner syndrome (MTS).METHODSA total of 173 patients who presented with MTS were retrospectively analyzed at a single center. Computed tomographic venography (CTV) was used to diagnose MTS. An AIVC was defined as the compression of the left common iliac vein (LCIV) by structures other than the right common iliac artery (RCIA) or the compression of other venous structures in the pelvic cavity instead of the LCIV. The patients with AIVC were categorized into the LCIV compression group (category A) and non-LCIV compression group (category B).RESULTSTen patients with AIVC were identified (5.8%; male/female, 5/5), five in category A and five in category B. The median age of patients was 76 years (range, 51–94 years), and the median follow-up duration was 388 days (range, 12–4694 days). In category A, the LCIVs were compressed by the left common iliac artery (LCIA) (n=2), uterine leiomyoma (n=1), LCIA aneurysm (n=1), and RCIA aneurysm (n=1). In category B, the right common iliac veins were compressed by the RCIA (n=4) and L5 osteophyte (n=1). Endovascular treatment, including balloon angioplasty and stent placement, was performed in six patients, three from each group. Three patients underwent conservative treatment due to their advanced age and comorbidities. Endovascular aneurysm repair was performed in one patient with RCIA aneurysm. Follow-up images were available for six patients, and all of them had patent venous flow.CONCLUSIONThe AIVC had an incidence of 5.8% (10/173) among symptomatic MTS patients and wide spectrum of etiologies. Pathogenesis-tailored endovascular treatments are safe and effective

Development of cDNA-derived SSR markers and their efficiency in diversity assessment of Cymbidium accessions

Abstract Cymbidium spp. are popular flowering plants. Assessment of the genetic diversity in cultivated Cymbidium facilitates conservation of germplasm and subsequent cultivar improvement. Thus, it is important to develop more efficient polymorphic DNA markers. Although more motifs (403) were identified and more primers (206) were designed in the genomic library compared to the cDNA library, a larger number of successful primers were obtained from the cDNA library (59.9%) than from genomic DNA library (51.1%). However, higher PIC and gene diversity were identified in genomic SSRs. The average allele number per locus was also higher in genomic SSRs (7.3) than EST-SSRs (5.2), among the 24 evaluated Cymbidium accessions. AT/TA was comparatively high in EST-SSRs, while this motif was not as common in genomic SSRs. The CTT/AAG/TCT/AGA/TTC/GAA and TGC/GCA/GCT/AGC/CTG/CAG motifs were the most abundant tri-nucleotide sequences in EST-SSRs, while GTT/AAC/TGT/ACA/TTG/CAA was the most frequent in genomic SSRs. The number of repeats ranged from 3 to 12 in EST-SSRs. Currently, 52 novel polymorphic SSR markers have been evaluated, which will be useful for germplasm assessments, core set construction, evaluation of genetic diversity, and marker assisted selection (MAS) based Cymbidium breeding

A Case of Non-Hodgkin's Lymphoma in Patient with Coombs' Negative Hemolytic Anemia and Idiopathic Thrombocytopenic Purpura

Coombs' negative autoimmune hemolytic anemia (AIHA) is a rare disease which shares similar clinical and hematological features with Coombs' positive AIHA, but its exact frequency remains unknown. There have been few reports of idiopathic thrombocytopenic purpura (ITP) and Coombs' negative AIHA associated with other lymphoproliferative disorders (LPDs). Since there is a well known association between LPDs and autoimmune phenomena, it is important to investigate the possibility of an underlying malignancy. We report a case of ITP and Coombs' negative AIHA associated with diffuse large B-cell lymphoma

Optical and microstructural studies of atomically flat ultrathin In-rich InGaN/GaN multiple quantum wells

Optical and microstructural properties of atomically flat ultrathin In-rich (UTIR) InGaN/GaN multiple quantum well were investigated by means of photoluminescence (PL), time-resolved PL (TRPL), and cathodoluminescence (CL) experiments. The sample exhibits efficient trapping of the photoexcited carriers into quantum wells (QWs) and the effect of internal electric field in the QWs was found negligible by excitation power-dependent PL and TRPL. These phenomena were attributed to the nature of UTIR InGaN QWs, indicating the potential of this system for application in optoelectronic devices. Variation of TRPL lifetime across the PL band and spatially resolved monochromatic CL mapping images strongly suggest that there is micrometer-scale inhomogeneity in effective band gap in UTIR InGaN/GaN QWs, which is originated from two types of localized areas.open141

Controlling Ferromagnetic Easy Axis in a Layered MoS2 Single Crystal

We report the effective methods to induce weak ferromagnetism in pristine MoS2 persisting up to room temperature with the improved transport property, which would lead to new spintronics devices. The hydrogenation of MoS2 by heating at 300 degrees C for 1 h leads to the easy axis out of plane, while the irradiation of proton with a dose of 1 x 10(13) P/cm(2) leads to the easy axis in plane. The theoretical modeling supports such magnetic easy axes.open16