Biomedical subjects

Bin Han

Publications and source records attributed to Bin Han.

44 records · Page 3Linked to original sources

PubMed2003

[Characterization of the copy number of RIRE10 retrotransposon and transcriptional activity of its LTR in rice genome].

A full-length Ty3-like retrotransposon, named RIRE10, was identified on the long arm of chromosome 4 in rice genome. The internal region between two LTRs had another open reading frame in the region upstream of gag-pol sequence. The transcripts from LTR region were detected by Northern blot hybridization and RT-PCR. To assess the activity of RIRE10 in rice genome, the copy number of its internal region and long terminal repeat (LTR) domain were determined by dot blot analyses. Nearly 900 solo-LTR of the RIRE10 retrotransposon exist in rice genome, apart from those LTRs that flank 65 intact RIRE retrotransposons. Based on the experimental results, the retrotransposition of RIRE10 was speculated to be influenced by two factors: transcriptional activity of LTR region and homologous recombination resulting in solo-LTR.

Amino Acid Sequence↗

PubMed2002

Sequence and analysis of rice chromosome 4.

Rice is the principal food for over half of the population of the world. With its genome size of 430 megabase pairs (Mb), the cultivated rice species Oryza sativa is a model plant for genome research. Here we report the sequence analysis of chromosome 4 of O. sativa, one of the first two rice chromosomes to be sequenced completely. The finished sequence spans 34.6 Mb and represents 97.3% of the chromosome. In addition, we report the longest known sequence for a plant centromere, a completely sequenced contig of 1.16 Mb corresponding to the centromeric region of chromosome 4. We predict 4,658 protein coding genes and 70 transfer RNA genes. A total of 1,681 predicted genes match available unique rice expressed sequence tags. Transposable elements have a pronounced bias towards the euchromatic regions, indicating a close correlation of their distributions to genes along the chromosome. Comparative genome analysis between cultivated rice subspecies shows that there is an overall syntenic relationship between the chromosomes and divergence at the level of single-nucleotide polymorphisms and insertions and deletions. By contrast, there is little conservation in gene order between rice and Arabidopsis.

Arabidopsis↗

PubMed2002

An F-box gene linked to the self-incompatibility (S) locus of Antirrhinum is expressed specifically in pollen and tapetum.

In many flowering plants, self-fertilization is prevented by an intraspecific reproductive barrier known as self-incompatibility (SI), that, in most cases, is controlled by a single multiallelic S locus. So far, the only known S locus product in self-incompatible species from the Solanaceae, Scrophulariaceae and Rosaceae is a class of ribonucleases called S RNases. Molecular and transgenic analyses have shown that S RNases are responsible for pollen rejection by the pistil but have no role in pollen expression of SI, which appears to be mediated by a gene called the pollen self-incompatibility or Sp gene. To identify possible candidates for this gene, we investigated the genomic structure of the S locus in Antirrhinum, a member of the Scrophulariaceae. A novel F-box gene, AhSLF-S2, encoded by the S2 allele, with the expected features of the Sp gene was identified. AhSLF-S2 is located 9 kb downstream of S2 RNase gene and encodes a polypeptide of 376 amino acids with a conserved F-box domain in its amino-terminal part. Hypothetical genes homologous to AhSLF-S2 are apparent in the sequenced genomic DNA of Arabidopsis and rice. Together, they define a large gene family, named SLF (S locus F-box) family. AhSLF-S2 is highly polymorphic and is specifically expressed in tapetum, microspores and pollen grains in an allele-specific manner. The possibility that Sp encodes an F-box protein and the implications of this for the operation of self-incompatibility are discussed.

Alleles↗

PubMed2002

A fibrin-based bioengineered ocular surface with human corneal epithelial stem cells.

PURPOSE: The purpose of the investigation was to prepare a bioengineered ocular surface tissue replacement consisting of (presumed) human corneal epithelial stem cells in a cross-linked fibrin gel for potential transplant. METHODS: Presumed human epithelial stem cells were harvested, isolated, and cultivated as previously described from adult donor corneas obtained from a tissue and organ bank. The cultured corneal epithelial stem cells were suspended in a fibronectin/fibrin gel cross-linked by factor XIII. Plasma components were derived from a fibrinogen-rich cryoprecipitate of human plasma. Suspended cells proliferated in the fibrin gel, giving rise to colonies that eventually coalesced to near confluence over the 15 days of cultivation. The gels were sectioned and immunostained for keratin 3 (AE5) and keratin 19. RESULTS: The fibrin gel product with corneal stem cells was easily manageable and maneuverable. Addition of the protease inhibitor aprotinin to the incubation medium prevented gel degradation; once it was removed, gels disintegrated within 24 hours. All of the cells cultivated in the fibrin gel stained positively for keratin 3 (AE5), indicating differentiation along the corneal epithelium lineage. Cells located in the center of the colonies were keratin 19-positive, suggesting a more primitive cell type. Growth kinetics were documented. CONCLUSIONS: A bioengineered ocular surface with a combination of presumed corneal epithelial stem cells in a cross-linked fibrin gel represents a potential improvement in current attempts to create a transportable, pliable, and stable tissue replacement. Since both the cells and the plasma components of the fibrin gel are of human origin, this technique provides the potential for a totally autologous bioengineered replacement tissue.

Adult↗

PubMed2002

A fine physical map of the rice chromosome 4.

As part of an international effort to completely sequence the rice genome, we have produced a fine bacterial artificial chromosome (BAC)-based physical map of the Oryza sativa japonica Nipponbare chromosome 4 through an integration of 114 sequenced BAC clones from a taxonomically related subspecies O. sativa indica Guangluai 4 and 182 RFLP and 407 expressed sequence tag (EST) markers with the fingerprinted data of the Nipponbare genome. The map consists of 11 contigs with a total length of 34.5 Mb covering 94% of the estimated chromosome size (36.8 Mb). BAC clones corresponding to telomeres, as well as to the centromere position, were determined by BAC-pachytene chromosome fluorescence in situ hybridization (FISH). This gave rise to an estimated length ratio of 5.13 for the long arm and 2.9 for the short arm (on the basis of the physical map), which indicates that the short arm is a highly condensed one. The FISH analysis and physical mapping also showed that the short arm and the pericentromeric region of the long arm are rich in heterochromatin, which occupied 45% of the chromosome, indicating that this chromosome is likely very difficult to sequence. To our knowledge, this map provides the first example of a rapid and reliable physical mapping on the basis of the integration of the data from two taxonomically related subspecies.

Chromosomes↗

PubMed2001

Identification and Structural Analysis of a Class of Potentially Transposable Solo-LTR in Rice Genome.

Two solo-LTRs, named SLTR1 and SLTR2, were found in BAC t17804 and q5343 on rice chromosome 4, respectively. SLTR1 is in a 18 S rRNA gene and SLTR2 is in a retrotransposon. They share sequence homology and show sequence similarity 89.1% and 70.1% to the LTR of rice retrotransposon RIRE8, respectively. SLTR1 and SLTR2 are of gypsy retrotransposons of rice. They are both highly repetitive sequences and widely distributed in the rice genome, as shown by hybridization with specific probes of SLTR1 and SLTR2. Using PCR amplication with primers on flanking sequences of SLTR1 and SLTR2, no bands corresponding to those of BACs were amplified using the rice genomic DNA as template. SLTR1 and SLTR2 did not locate in the relative loci of the rice genome, as supported by hybridization with specific probes of genes interrupted by them. Obviously, SLTR1 and SLTR2 reported here came from different loci of the genome by the transposition. These solo-LTRs may be useful for our rice genome studies.

Journal Article↗

PubMed2001

Structural Analysis of a Gene Cluster Encoding Two Cationic and Three Anionic Peroxidases from Rice Chromosome 4.

Sequence analysis of a rice BAC q3037(H0207F01) identified a cluster of five tandemly arranged peroxidase genes, osp1,osp2,osp3,osp4 and osp5, within a 22.5 kb region. osp4,osp5 each have three exons interrupted by two introns, while osp1,osp2 and osp3 each have two exons interrupted by a single intron. The five genes were predicted products of 338, 335, 336, 343 and 346 amino acid residues, respectively, including putative signal peptide sequence at the amino-termini. And OSP1, OSP4 and OSP5 were predicted to be anionic peroxidase, OSP2 and OSP3 are cationic. Comparative analysis and evolutionary analysis of the clustered genes and other peroxidase family members revealed that the gene cluster occurred by tandemly gene duplications(from osp5 to osp1) and that osp5,ap1 and prx7 were potential orthologies, and osp1-5, ap1 and prx7 constituted a novel evolutionary branch of class III peroxidases.

Journal Article↗

PubMed2000

CT finding is an index in assessment of outcome in patients with diffuse traumatic brain swelling.

OBJECTIVE: To assess the relationship between the prognosis of the patients with diffuse traumatic brain swelling (DTBS) and the changes of the ventricles and the cisterns in CT scans. METHODS: The outcome of the patients with DTBS and the changes of the ventricles and the cisterns in CT scans were studied and analyzed in a group of 268 cases. We focused on the changes of the third ventricle and the basal cistern, age and Glasgow Coma Scale (GCS). RESULTS: Of 268 cases, there were changes of the third ventricle and/or the basal cistern in 124, 65 died. In l8 cases, the third ventricle and the basal cistern were both absent and l6 died (88.9%). The third ventricle changed significantly in 59 cases, 33 died (55.9%), while the basal cistern changed in 47 cases and 16 died (34%). Of the 124 patients with changes of the third ventricle and/or the basal cistern, 26 were children, 8 died; 98 adults, 57 died. CONCLUSIONS: For patients with DTBS, the outcome was in direct correlation with the change of the third ventricle and/or the basal cistern, the change of the third ventricle was much more important in assessment of the outcome than that of basal cisterns. There is no significant difference in, the incidence of DTBS between children and adults while the outcome of children is much better than that of adults. The patients with the changes of the third ventricle and the basal cistern accompanied with lower GCS scores have poor outcome.

Journal Article↗