Optical Transitions of a Single Nodal Ring in SrAs_{3}: Radially and Axially Resolved Characterization.

SrAs_{3} is a unique nodal-line semimetal that contains only a single nodal ring in the Brillouin zone, uninterrupted by any trivial bands near the Fermi energy. We performed axis-resolved optical reflection measurements on SrAs_{3} and observed that the optical conductivity exhibits flat absorption up to 129 meV in both the radial and axial directions, confirming the robustness of the universal power-law behavior of the nodal ring. The axis-resolved optical conductivity, in combination with theoretical calculations, further reveals fundamental properties beyond the flat absorption, including the overlap energy of the topological bands, the spin-orbit coupling gap along the nodal ring, and the geometric properties of the nodal ring such as the average ring radius, ring ellipticity, and velocity anisotropy. In addition, our temperature-dependent measurements revealed a spectral weight transfer between intraband and interband transitions, indicating a possible violation of the optical sum rule within the measured energy range.

Quantum transport evidence of isolated topological nodal-line fermions.

Anomalous transport responses, dictated by the nontrivial band topology, are the key for application of topological materials to advanced electronics and spintronics. One promising platform is topological nodal-line semimetals due to their rich topology and exotic physical properties. However, their transport signatures have often been masked by the complexity in band crossings or the coexisting topologically trivial states. Here we show that, in slightly hole-doped SrAs3, the single-loop nodal-line states are well-isolated from the trivial states and entirely determine the transport responses. The characteristic torus-shaped Fermi surface and the associated encircling Berry flux of nodal-line fermions are clearly manifested by quantum oscillations of the magnetotransport properties and the quantum interference effect resulting in the two-dimensional behaviors of weak antilocalization. These unique quantum transport signatures make the isolated nodal-line fermions in SrAs3 desirable for novel devices based on their topological charge and spin transport.

Accessing the Intrinsic Spin Transport in a Topological Insulator by Controlling the Crossover of Bulk-to-Surface Conductance.

We report a method to control contributions of bulk and surface states in the topological insulator Bi_{2}Te_{2}Se that allows accessing the spin-polarized transport endowed by topological surface states. An intrinsic surface dominant transport is established when cooling the sample to low temperature or reducing the conduction channel length, both achieved in situ in the transport measurements with a four-probe scanning tunneling microscope without the need of further tailoring the sample. The topological surface states show characteristic transport behaviors with mobility about an order of magnitude higher than reported before, and a spin polarization approaching the theoretically predicted value. Our result demonstrates accessibility to the intrinsic high mobility spin transport of topological surface states, which paves a way to realizing topological spintronic devices.

Generation, transport and detection of valley-locked spin photocurrent in WSe2-graphene-Bi2Se3 heterostructures.

Quantum optoelectronic devices capable of isolating a target degree of freedom (DoF) from other DoFs have allowed for new applications in modern information technology. Many works on solid-state spintronics have focused on methods to disentangle the spin DoF from the charge DoF1, yet many related issues remain unresolved. Although the recent advent of atomically thin transition metal dichalcogenides (TMDs) has enabled the use of valley pseudospin as an alternative DoF2,3, it is nontrivial to separate the spin DoF from the valley DoF since the time-reversal valley DoF is intrinsically locked with the spin DoF4. Here, we demonstrate lateral TMD-graphene-topological insulator hetero-devices with the possibility of such a DoF-selective measurement. We generate the valley-locked spin DoF via a circular photogalvanic effect in an electric-double-layer WSe2 transistor. The valley-locked spin photocarriers then diffuse in a submicrometre-long graphene layer, and the spin DoF is measured separately in the topological insulator via non-local electrical detection using the characteristic spin-momentum locking. Operating at room temperature, our integrated devices exhibit a non-local spin polarization degree of higher than 0.5, providing the potential for coupled opto-spin-valleytronic applications that independently exploit the valley and spin DoFs.

The first generation of a BAC-based physical map of Brassica rapa.

BACKGROUND: The genus Brassica includes the most extensively cultivated vegetable crops worldwide. Investigation of the Brassica genome presents excellent challenges to study plant genome evolution and divergence of gene function associated with polyploidy and genome hybridization. A physical map of the B. rapa genome is a fundamental tool for analysis of Brassica "A" genome structure. Integration of a physical map with an existing genetic map by linking genetic markers and BAC clones in the sequencing pipeline provides a crucial resource for the ongoing genome sequencing effort and assembly of whole genome sequences. RESULTS: A genome-wide physical map of the B. rapa genome was constructed by the capillary electrophoresis-based fingerprinting of 67,468 Bacterial Artificial Chromosome (BAC) clones using the five restriction enzyme SNaPshot technique. The clones were assembled into contigs by means of FPC v8.5.3. After contig validation and manual editing, the resulting contig assembly consists of 1,428 contigs and is estimated to span 717 Mb in physical length. This map provides 242 anchored contigs on 10 linkage groups to be served as seed points from which to continue bidirectional chromosome extension for genome sequencing. CONCLUSION: The map reported here is the first physical map for Brassica "A" genome based on the High Information Content Fingerprinting (HICF) technique. This physical map will serve as a fundamental genomic resource for accelerating genome sequencing, assembly of BAC sequences, and comparative genomics between Brassica genomes. The current build of the B. rapa physical map is available at the B. rapa Genome Project website for the user community.

Hepatic cyst misdiagnosed as a gastric submucosal tumor: a case report.

We describe here a case of 51-year-old woman with a symptomatic hepatic cyst that was misdiagnosed as a gastric submucosal tumor (SMT) with endoscopic ultrasound (EUS) and CT scan. The patient presented with an epigastric pain for two months. On endoscopy, a submucosal tumor was found on the cardia of the stomach. Based on EUS and abdominal CT scan, the lesion was diagnosed as a gastric duplication cyst or a gastrointestinal stromal tumor (GIST). The operative plan was laparoscopic wedge resection for the GIST of the gastric cardia. A cystic mass arising from the left lateral segment of the liver was found at the laparoscopic examination. There was no abnormal finding at the gastric cardia. She was treated by laparoscopic hepatic wedge resection including the hepatic cyst using an endoscopic linear stapler.

Terminal repeat retrotransposon in miniature (TRIM) as DNA markers in Brassica relatives.

We have developed a display system using a unique sequence of terminal repeat retrotransposon in miniature (TRIM) elements, which were recently identified from gene-rich regions of Brassica rapa. The technique, named TRIM display, is based on modification of the AFLP technique using an adapter primer for the restriction fragments of BfaI and a primer derived from conserved terminal repeat sequences of TRIM elements, Br1 and Br2. TRIM display using genomic DNA produced 50-70 bands ranging from 100 to 700 bp in all the species of the family Brassicaceae. TRIM display using B. rapa cDNA produced about 20 bands. Sequences of 11 randomly selected bands, 7 from genomic DNA and 4 from cDNA, begin with about 104 bp of the terminal repeat sequences of TRIM elements Br1 or Br2 and end with unique sequences indicating that all bands are derived from unique insertion sites of TRIM elements. Furthermore, 7 of the 11 unique sequences showed significant similarity with expressed gene. Most of the TRIM display bands were polymorphic between genera and about 55% (132 of 239 bands) are polymorphic among 19 commercial F1 hybrid cultivars. Analysis of phylogenetic relationships shows clear-cut lineage among the 19 cultivars. Furthermore, a combination of 11 polymorphic bands derived from only one primer combination can clearly distinguish one cultivar from the others. TRIM display bands were reproducible and inheritable through successive generations that is revealed by genetic mapping of 6 out of 27 polymorphic TRIM markers on the genetic map of Brassica napus. Collective data provide evidence that TRIM display can provide useful DNA markers in Brassica relatives because these markers are distributed in gene-rich regions, and are sometimes involved in the restructuring of genes.

Isolation of circadian-associated genes in Brassica rapa by comparative genomics with Arabidopsis thaliana.

Elucidation of the roles of circadian associated factors requires a better understanding of the molecular mechanisms of circadian rhythms, control of flowering time through photoperiodic pathways, and photosensory signal transduction. In Arabidopsis, the APRR1 quintet, APRRs 1, 3, 5, 7, and 9, are known as central oscillator genes. Other plants may share the molecular mechanism underlying the circadian rhythm. To identify and characterize these circadian response genes in Brassica crops whose genome was triplicated after divergence from Arabidopsis, we identified B. rapa BAC clones containing these genes by BLAST analysis of B. rapa BAC end sequences against the five corresponding Arabidopsis regions. Subsequent fingerprinting, Southern hybridization, and PCR allowed identification of five BAC clones, one for each of the five circadian-related genes. By draft shotgun sequencing of the BAC clones, we identified the complete gene sequences and cloned the five expressed B. rapa circadian-associated gene members, BrPRRs 1, 3, 5, 7, and 9. Phylogenetic analysis revealed that each BrPRR was orthologous to the corresponding APRR at the sequence level. Northern hybridization revealed that the five genes were transcribed at distinct points in the 24 hour period, and Southern hybridization revealed that they are present in 2, 1, 2, 2, and 1 copies, respectively in the B. rapa genome, which was triplicated and then diploidized during the last 15 million years.

Characterization of terminal-repeat retrotransposon in miniature (TRIM) in Brassica relatives.

We have newly identified five Terminal-repeat retrotransposon in miniature (TRIM) families, four from Brassica and one from Arabidopsis. A total of 146 elements, including three Arabidopsis families reported before, are extracted from genomics data of Brassica and Arabidopsis, and these are grouped into eight distinct lineages, Br1 to Br4 derived from Brassica and At1 to At4 derived from Arabidopsis. Based on the occurrence of TRIM elements in 434 Mb of B. oleracea shotgun sequences and 96 Mb of B. rapa BAC end sequences, total number of TRIM members of Br1, Br2, Br3, and Br4 families are roughly estimated to be present in 660 and 530 copies in B. oleracea and B. rapa genomes, respectively. Studies on insertion site polymorphisms of four elements across taxa in the tribe Brassiceae infer the taxonomic lineage and dating of the insertion time. Active roles of the TRIM elements for evolution of the duplicated genes are inferred in the highly replicated Brassica genome.

Characterization of the centromere and peri-centromere retrotransposons in Brassica rapa and their distribution in related Brassica species.

We report the identification and characterization of the major repeats in the centromeric and peri-centromeric heterochromatin of Brassica rapa. The analysis involved the characterization of 88 629 bacterial artificial chromosomes (BAC) end sequences and the complete sequences of two BAC clones. We identified centromere-specific retrotransposons of Brassica (CRB) and various peri-centromere-specific retrotransposons (PCRBr). Three copies of the CRB were identified in one BAC clone as nested insertions within a tandem array of 24 copies of a 176 bp centromeric repeat, CentBr. A complex mosaic structure consisting of nine PCRBr elements and large blocks of 238 bp degenerate tandem repeats (TR238) were found in or near a derivative of 5S-25S rDNA sequences. The chromosomal positions of selected repeats were determined using in situ hybridization. These revealed that CRB is a major component of all centromeres in three diploid Brassica species and their allotetraploid relatives. However, CentBr was not detected in the most distantly related of the diploid species analyzed, B. nigra. PCRBr and TR238 were found to be major components in the peri-centromeric heterochromatin blocks of four chromosomes of B. rapa. These repetitive elements were not identified in B. oleracea or B. nigra, indicating that they are A-genome-specific. GenBank accession numbers: KBrH001P13 (AC 166739); KBrH015B20 (AC 166740); end sequences of KBrH BAC library (CW 978640 - CW 988843); end sequences of KBrS BAC library (DU 826965 - DU 835595); end sequences of KBrB BAC library (DX 010661 - DX 083363).

A sequence-tagged linkage map of Brassica rapa.

A detailed genetic linkage map of Brassica rapa has been constructed containing 545 sequence-tagged loci covering 1287 cM, with an average mapping interval of 2.4 cM. The loci were identified using a combination of 520 RFLP and 25 PCR-based markers. RFLP probes were derived from 359 B. rapa EST clones and amplification products of 11 B. rapa and 26 Arabidopsis. Including 21 SSR markers provided anchors to previously published linkage maps for B. rapa and B. napus and is followed as the referenced mapping of R1-R10. The sequence-tagged markers allowed interpretation of the pattern of chromosome duplications within the B. rapa genome and comparison with Arabidopsis. A total of 62 EST markers showing a single RFLP band were mapped through 10 linkage groups, indicating that these can be valuable anchoring markers for chromosome-based genome sequencing of B. rapa. Other RFLP probes gave rise to 2-5 loci, inferring that B. rapa genome duplication is a general phenomenon through 10 chromosomes. The map includes five loci of FLC paralogues, which represent the previously reported BrFLC-1, -2, -3, and -5 and additionally identified BrFLC3 paralogues derived from local segmental duplication on R3.

Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa.

Strong evidence exists for polyploidy having occurred during the evolution of the tribe Brassiceae. We show evidence for the dynamic and ongoing diploidization process by comparative analysis of the sequences of four paralogous Brassica rapa BAC clones and the homologous 124-kb segment of Arabidopsis thaliana chromosome 5. We estimated the times since divergence of the paralogous and homologous lineages. The three paralogous subgenomes of B. rapa triplicated 13 to 17 million years ago (MYA), very soon after the Arabidopsis and Brassica divergence occurred at 17 to 18 MYA. In addition, a pair of BACs represents a more recent segmental duplication, which occurred approximately 0.8 MYA, and provides an exception to the general expectation of three paralogous segments within the B. rapa genome. The Brassica genome segments show extensive interspersed gene loss relative to the inferred structure of the ancestral genome, whereas the Arabidopsis genome segment appears little changed. Representatives of all 32 genes in the Arabidopsis genome segment are represented in Brassica, but the hexaploid complement of 96 has been reduced to 54 in the three subgenomes, with compression of the genomic region lengths they occupy to between 52 and 110 kb. The gene content of the recently duplicated B. rapa genome segments is identical, but intergenic sequences differ.

Gastric cancer confined to the muscularis propria: a possible candidate for laparoscopic surgery or adjuvant therapy.

OBJECTIVE: Gastric cancer confined to the muscularis propria (mp) has a favorable prognosis, but still belongs to the advanced category. Many oncologists have difficulties in selecting treatment modalities owing to the confused situation of mp cancer. To clarify the therapeutic strategy, the clinicopathological characteristics were investigated, and the risk factors, of this intermediate-stage gastric cancer, evaluated. MATERIAL AND METHODS: A total of 155 patients who underwent curative resection for primary gastric cancer between 1993 and 2001 were diagnosed with mp cancer. The patients were divided into recurrent and non-recurrent groups and analyzed clinicopathologically. RESULTS: The rate of recurrence was 20%. A multivariate analysis disclosed only lymphatic metastasis as an independent risk factor for recurrence of mp cancer. Hematogenous metastasis accounted for 37% of the recurrent patterns, and the liver (83.3%) was the most common organ. The 5-year survival rate of all mp cancer patients was 80.9%, but that of patients with recurrent disease was 19.2%. The median survival time of the recurred patients was 24 months, and 74% of those patients died within 3 years. CONCLUSIONS: Lymph node metastasis is the only significant risk factor of mp cancer. Patients with lymphatic metastasis should undergo postoperative adjuvant therapy. On the other hand, patients with mp cancer without lymph node involvement have an excellent prognosis and could be candidates for laparoscopic gastric surgery.

Characterization of rDNAs and tandem repeats in the heterochromatin of Brassica rapa.

We describe the morphology and molecular organization of heterochromatin domains in the interphase nuclei, and mitotic and meiotic chromosomes, of Brassica rapa, using DAPI staining and fluorescence in situ hybridization (FISH) of rDNA and pericentromere tandem repeats. We have developed a simple method to distinguish the centromeric regions of mitotic metaphase chromosomes by prolonged irradiation with UV light at the DAPI excitation wavelength. Application of this bleached DAPI band (BDB) karyotyping method to the 45S and 5S rDNAs and 176 bp centromere satellite repeats distinguished the 10 B. rapa chromosomes. We further characterized the centromeric repeat sequences in BAC end sequences. These fell into two classes, CentBr1 and CentBr2, occupying the centromeres of eight and two chromosomes, respectively. The centromere satellites encompassed about 30% of the total chromosomes, particularly in the core centromere blocks of all the chromosomes. Interestingly, centromere length was inversely correlated with chromosome length. The morphology and molecular organization of heterochromatin domains in interphase nuclei, and in mitotic and meiotic chromosomes, were further characterized by DAPI staining and FISH of rDNA and CentBr. The DAPI fluorescence of interphase nuclei revealed ten to twenty conspicuous chromocenters, each composed of the heterochromatin of up to four chromosomes and/or nucleolar organizing regions.

The Korea brassica genome project: a glimpse of the brassica genome based on comparative genome analysis with Arabidopsis.

A complete genome sequence provides unlimited information in the sequenced organism as well as in related taxa. According to the guidance of the Multinational Brassica Genome Project (MBGP), the Korea Brassica Genome Project (KBGP) is sequencing chromosome 1 (cytogenetically oriented chromosome #1) of Brassica rapa. We have selected 48 seed BACs on chromosome 1 using EST genetic markers and FISH analyses. Among them, 30 BAC clones have been sequenced and 18 are on the way. Comparative genome analyses of the EST sequences and sequenced BAC clones from Brassica chromosome 1 revealed their homeologous partner regions on the Arabidopsis genome and a syntenic comparative map between Brassica chromosome 1 and Arabidopsis chromosomes. In silico chromosome walking and clone validation have been successfully applied to extending sequence contigs based on the comparative map and BAC end sequences. In addition, we have defined the (peri)centromeric heterochromatin blocks with centromeric tandem repeats, rDNA and centromeric retrotransposons. In-depth sequence analyses of five homeologous BAC clones and an Arabidopsis chromosomal region reveal overall co-linearity, with 82% sequence similarity. The data indicate that the Brassica genome has undergone triplication and subsequent gene losses after the divergence of Arabidopsis and Brassica. Based on in-depth comparative genome analyses, we propose a comparative genomics approach for conquering the Brassica genome. In 2005 we intend to construct an integrated physical map, including sequence information from 500 BAC clones and integration of fingerprinting data and end sequence data of more than 100,000 BAC clones.