Biomedical subjects

Bin Han

Publications and source records attributed to Bin Han.

At least 37 records · Page 2Linked to original sources

PubMed2005

Isolation and annotation of 10828 putative full length cDNAs from indica rice.

We reported the isolation and identification of 10828 putative full-length cDNAs (FL-cDNA) from an indica rice cultivar, Minghui 63, with the long-term goal to isolate all full-length cDNAs from indica genome. Comparison with the databases showed that 780 of them are new rice cDNAs with no match in japonica cDNA database. Totally, 9078 of the FL-cDNAs contained predicted ORFs matching with japonica FL-cDNAs and 6543 could find homologous proteins with complete ORFs. 53% of the matched FL-cDNAs isolated in this study had longer 5'UTR than japonica FL-cDNAs. In silico mapping showed that 9776 (90.28%) of the FL-cDNAs had matched genomic sequences in the japonica genome and 10046 (92.78%) had matched genomic sequences in the indica genome. The average nucleotide sequence identity between the two subspecies is 99.2%. A majority of FL-cDNAs (90%) could be classified with GO (gene ontology) terms based on homology proteins. More than 60% of the new cDNAs isolated in this study had no homology to the known proteins. This set of FL-cDNAs should be useful for functional genomics and proteomics studies.

DNA, Complementary↗

PubMed2005

[Effects of genotype and environment on protein and starch quality of wheat grain].

A field trial with 10 winter wheat varieties was conducted at 9 locations under different environmental conditions in Shandong Province to study the effects of wheat genotype and environment on the main qualitative characters of wheat grain. The results indicated that variety and environment had a marked influence on the main qualitative indexes of wheat grain, and the difference of environmental conditions was the main factor affecting the protein and gluten contents of the grain. The variation of farinogramme indexes was mainly due to the interaction between variety and environment. As for the starch content, peak viscosity, and breakdown of the grain, interactive effect was stronger than independent one, and the effect of variety was stronger than that of environment.

Environment↗

PubMed2004

Epoxide hydrolase-catalyzed enantioselective synthesis of chiral 1,2-diols via desymmetrization of meso-epoxides. lzhao@diversa.com.

The discovery, from nature, of a diverse set of microbial epoxide hydrolases is reported. The utility of a library of epoxide hydrolases in the synthesis of chiral 1,2-diols via desymmetrization of a wide range of meso-epoxides, including cyclic as well as acyclic alkyl- and aryl-substituted substrates, is demonstrated. The chiral (R,R)-diols were furnished with high ee's and yields. The discovery of the first microbial epoxide hydrolases providing access to complementary (S,S)-diols is also described.

Alcohols↗

PubMed2004

Molecular cytogenetic characterization of the Antirrhinum majus genome.

As a model system in classical plant genetics, the genus Antirrhinum has been well studied, especially in gametophytic self-incompatibility, flower development biology, and transposon-induced mutation. In contrast to the advances in genetic and molecular studies, little is known about Antirrhinum cytogenetics. In this study, we isolated two tandem repetitive sequences, CentA1 and CentA2, from the centromeric regions of Antirrhinum chromosomes. A standard karyotype has been established by anchoring these centromeric repeats on meiotic pachytene chromosome using FISH. An ideogram based on the DAPI-staining pattern of pachytene chromosomes was developed to depict the distribution of heterochromatin in the Antirrhinum majus genome. To integrate the genetic and chromosomal maps, we selected one or two molecular markers from each linkage group to screen an Antirrhinum transformation-competent artificial chromosome (TAC) library. These genetically anchored TAC clones were labeled as FISH probes to hybridize to pachytene chromosomes of A. majus. As a result, the relationship between chromosomes and the linkage groups (LGs) in Antirrhinum has been established.

Antirrhinum↗

PubMed2004

Preparation of single rice chromosome for construction of a DNA library using a laser microbeam trap.

We report the development of a laser micromanipulation system and its application in the isolation of individual rice chromosomes directly from a metaphase cell. Microdissection and flow sorting are two major methods for the isolation of single chromosome. These methods are dependent on the techniques of chromosome spread and chromosome suspension, respectively. In the development of this system, we avoided using chromosome spread and cell suspension was used instead. The cell wall of metaphase rice cell was cut by optical scissors. The released single chromosome was captured by an optical trap and transported to an area without cell debris. The isolated single chromosome was then collected and specific library was constructed by linker adaptor PCR. The average insert size of the library was about 300 bp. Two hundred inserts of chromosome 4 library were sequenced, and 96.5% were aligned to the corresponding sequences of rice chromosome 4. These results suggest the possible application of this method for the preparation of other subcellular structures and for the cloning of single macromolecule through a laser microbeam trap.

Chromosomes, Plant↗

PubMed2004

Structural features of the rice chromosome 4 centromere.

A complete sequence of a chromosome centromere is necessary for fully understanding centromere function. We reported the sequence structures of the first complete rice chromosome centromere through sequencing a large insert bacterial artificial chromosome clone-based contig, which covered the rice chromosome 4 centromere. Complete sequencing of the 124-kb rice chromosome 4 centromere revealed that it consisted of 18 tracts of 379 tandemly arrayed repeats known as CentO and a total of 19 centromeric retroelements (CRs) but no unique sequences were detected. Four tracts, composed of 65 CentO repeats, were located in the opposite orientation, and 18 CentO tracts were flanked by 19 retroelements. The CRs were classified into four types, and the type I retroelements appeared to be more specific to rice centromeres. The preferential insert of the CRs among CentO repeats indicated that the centromere-specific retroelements may contribute to centromere expansion during evolution. The presence of three intact retrotransposons in the centromere suggests that they may be responsible for functional centromere initiation through a transcription-mediated mechanism.

Base Sequence↗

PubMed2004

Transcript abundance of rml1, encoding a putative GT1-like factor in rice, is up-regulated by Magnaporthe grisea and down-regulated by light.

We isolated and sequenced both genomic DNA and cDNA clones, which encoded a putative GT1-like protein with 385 amino acids, from cultivated rice (Oryza sativa ssp. indica). This protein shows significant amino acid sequence similarities with trihelix DNA-binding GT-1a/B2F and GT-1 factors that were identified in dicot plants. Northern blotting analysis indicated that the transcript of the rice GT-1 factor in seedling was up-regulated by the rice blast fungus Magnaporthe grisea, down-regulated by various continuous light conditions and expressed rhythmically in light/dark cycles. This GT1-like factor gene was therefore designated as rml1 (rice gene regulated by M. grisea and light). The putative RML1 protein, encoded by this single copy gene, is thus identified as a new member of the plant-specific GT family of transcription factors in rice.

Amino Acid Sequence↗

PubMed2004

Monitoring of gene expression profiles and isolation of candidate genes involved in pollination and fertilization in rice ( Oryza sativa L.) with a 10K cDNA microarray.

To monitor gene expression profiles during pollination and fertilization in rice at a genome scale, we generated 73,424 high-quality expressed sequence tags (ESTs) derived from the green/etiolated shoot and pistil (0-5 h after pollination, 5hP) of rice, which were subsequently used to construct a cDNA microarray containing ca. 10 000 unique rice genes. This microarray was used to analyze gene expression in pistil unpollinated (UP), 5hP and 5DAP(5 days after pollination), anther, shoot, root, 10-day-old embryo (10EM) and 10-day-old endosperm (10EN). Clustering analysis revealed that the anther has a gene-expression profile more similar to root than to pistil and most pistil-preferentially expressed genes respond to pollination and/or fertilization. There are 253 ESTs exhibiting differential expression (e +/- 2-fold changes) during pollination and fertilization, and about 70% of them can be assigned a putative function. We also recovered 20 genes similar to pollination-related and/or fertility-related genes previously identified as well as genes that were not implicated previously. Microarray and real-time PCR analyses showed that the array sensitivity was estimated at 1-5 copies of mRNA per cell, and the differentially expressed genes showed a high correlation between the two methods. Our results indicated that this cDNA microarray constructed here is reliable and can be used for monitoring gene expression profiles in rice. In addition, the genes that differentially expressed during pollination represent candidate genes for dissecting molecular mechanism of this important biological process in rice.

Cluster Analysis↗

PubMed2004

Dampable waves along nucleic acid sequences mediating nucleotides' interactions.

This work studied the relationship of any two nucleotides in genomic sequences, coding sequences and full-length cDNAs. We made a statistical hypothesis that there exist no interactions between any two nucleotides in sequences, therefore, a hypothetical combination distribution of two nucleotides is considered and the difference between the hypothetical combination distribution and the actual distribution is used to measure the average interaction between the two nucleotides. As a result, we found that the interactions between any two nucleotides are clearly and closely related with dampable wavelike patterns along the sequences. Based on the results we daringly make some hypotheses on several biological topics. Further, studies on the wave may provide new clues for gene prediction and genome structure study.

Algorithms↗

PubMed2004

We did the right thing: an intervention analysis approach to modeling intervened SARS propagation in Singapore.

In this paper, we adopt the Intervention Analysis approach to model an intervened natural process, i.e., propagation of the severe acute respiratory syndrome (SARS) in Singapore, which is affected not only by its own evolutionary history but also by the control measures taken. Using this model, the propagation trend of the epidemic and the effects of different control measures on the outcomes of this epidemic can be simulated and quantitatively analyzed. Based on the model, we have performed an evaluation and sensitivity analysis of the Singapore government's responses to this epidemic. Preliminary results have shown that the control measures taken are effective in controlling the outbreak.

Communicable Disease Control↗

PubMed2004

[Identification and analysis of a group of highly conserved trs-like genes in rice].

There are at least ten transcriptional trs-like genes in rice that have been confirmed by RT - PCR and sequencing, based on the annotation results of rice genome and homologous search. These ten genes correspond to six of the ten known subunits of TRAPP complex in yeast. Four pairs of them are duplicates while the other two are unique according to the known rice genomic sequences. All of the ten genes are constitutively expressed in rice tissues and share phylogenetic homology to some extent with other eukaryotic trs-like genes in their gene structures and protein sequences.

Genes, Plant↗

PubMed2004

[The structural, transcriptional and homology analysis of two frr genes in rice].

Two rice (Oryza sativa subsp. japonica cv. Nipponbare) ribosome recycling factor genes--OsfrrA and OsfrrB had been identified and characterized in this study. The gene OsfrrA is located on chromosome 4 while OsfrrB on chromosome 7. No other homologue is found in rice organelle genomes. Both genes are unique in rice genome and constitutively expressed. The N-terminal character of their encoded protein products suggests that the proteins are transferred to mitochondrion and chloroplast respectively and carry out their functions. The sequence conservation and the constitutive expression profile of the two genes strongly imply their indispensable role in plant growth. In addition, these sequences share phylogenetic homology to some extent with other prokaryotic and eukaryotic RRFs, providing further evidence for the endosymbiotic theory, and implying the potential value of RRFs in molecular evolution research.

Amino Acid Sequence↗

PubMed2003

Sequence variations of simple sequence repeats on chromosome-4 in two subspecies of the Asian cultivated rice.

Computational screening of the chromosome-4 sequence of the rice cultivar Nipponbare ( Oryza sativa L. japonica) revealed 1,844 tandem simple sequence repeats (SSRs) or microsatellites with SSR motifs >/=20 bp and repeated unit length of 1-6 base pairs. Thus SSRs occur once in every 18.8 kb, on the average, on the chromosome with one SSR per 23.8 kb and 16 kb on the short and long arms, respectively. No SSR was detected in the core region of the centromere. Poly(AT)(n) repeats represented the most abundant and length polymorphic class of SSRs on the chromosome, but it did not occur in the exons. GC-rich trinucleotide repeats were most abundant in the coding regions, representing 71.69% of the SSRs identified in the exons. Two hundred and twenty four SSRs were associated with the repetitive DNA sequences, most of them were poly(AT)(n) tracts. Sequence variations of SSRs between two cultivars, representing the two subspecies of the Asian cultivated rice indica and japonica, were identified, revealing that divergence and convergence of the two subspecies could be traced by the analysis of SSRs. These results provide a great opportunity for SSR-based marker development and comparative genome analysis of the two subspecies of the Asian cultivated rice.

Base Composition↗

PubMed2003

Gene expression phenotypes of Arabidopsis associated with sensitivity to low temperatures.

Chilling is a common abiotic stress that leads to economic losses in agriculture. By comparing the transcriptome of Arabidopsis under normal (22 degrees C) and chilling (13 degrees C) conditions, we have surveyed the molecular responses of a chilling-resistant plant to acclimate to a moderate reduction in temperature. The mRNA accumulation of approximately 20% of the approximately 8,000 genes analyzed was affected by chilling. In particular, a highly significant number of genes involved in protein biosynthesis displayed an increase in transcript abundance. We have analyzed the molecular phenotypes of 12 chilling-sensitive mutants exposed to 13 degrees C before any visible phenotype could be detected. The number and pattern of expression of chilling-responsive genes in the mutants were consistent with their final degree of chilling injury. The mRNA accumulation profiles for the chilling-lethal mutants chs1, chs2, and chs3 were highly similar and included extensive chilling-induced and mutant-specific alterations in gene expression. The expression pattern of the mutants upon chilling suggests that the normal function of the mutated loci prevents a damaging widespread effect of chilling on transcriptional regulation. In addition, we have identified 634 chilling-responsive genes with aberrant expression in all of the chilling-lethal mutants. This reference gene list, including genes related to lipid metabolism, chloroplast function, carbohydrate metabolism and free radical detoxification, represents a potential source for genes with a critical role in plant acclimation to suboptimal temperatures. The comparison of transcriptome profiles after transfer of Arabidopsis plants from 22 degrees C to 13 degrees C versus transfer to 4 degrees C suggests that quantitative and temporal differences exist between these molecular responses.

Acclimatization↗

PubMed2003

Control of tillering in rice.

Tillering in rice (Oryza sativa L.) is an important agronomic trait for grain production, and also a model system for the study of branching in monocotyledonous plants. Rice tiller is a specialized grain-bearing branch that is formed on the unelongated basal internode and grows independently of the mother stem (culm) by means of its own adventitious roots. Rice tillering occurs in a two-stage process: the formation of an axillary bud at each leaf axil and its subsequent outgrowth. Although the morphology and histology and some mutants of rice tillering have been well described, the molecular mechanism of rice tillering remains to be elucidated. Here we report the isolation and characterization of MONOCULM 1 (MOC1), a gene that is important in the control of rice tillering. The moc1 mutant plants have only a main culm without any tillers owing to a defect in the formation of tiller buds. MOC1 encodes a putative GRAS family nuclear protein that is expressed mainly in the axillary buds and functions to initiate axillary buds and to promote their outgrowth.

Agriculture↗

PubMed2003

Genome-wide intraspecific DNA-sequence variations in rice.

Genome-wide comparative analysis of the DNA sequences of two major cultivated rice subspecies, Oryza sativa L. ssp indica and Oryza sativa L. ssp japonica, have revealed their extensive microcolinearity in gene order and content. However, deviations from colinearity are frequent owing to insertions or deletions. Intraspecific sequence polymorphisms commonly occur in both coding and non-coding regions. These variations often affect gene structures and may contribute to intraspecific phenotypic adaptations.

Genetic Variation↗

PubMed2003

Quantitative nature of Arabidopsis responses during compatible and incompatible interactions with the bacterial pathogen Pseudomonas syringae.

We performed large-scale mRNA expression profiling using an Affymetrix GeneChip to study Arabidopsis responses to the bacterial pathogen Pseudomonas syringae. The interactions were compatible (virulent bacteria) or incompatible (avirulent bacteria), including a nonhost interaction and interactions mediated by two different avirulence gene-resistance (R) gene combinations. Approximately 2000 of the approximately 8000 genes monitored showed reproducible significant expression level changes in at least one of the interactions. Analysis of biological variation suggested that the system behavior of the plant response in an incompatible interaction was robust but that of a compatible interaction was not. A large part of the difference between incompatible and compatible interactions can be explained quantitatively. Despite high similarity between responses mediated by the R genes RPS2 and RPM1 in wild-type plants, RPS2-mediated responses were strongly suppressed by the ndr1 mutation and the NahG transgene, whereas RPM1-mediated responses were not. This finding is consistent with the resistance phenotypes of these plants. We propose a simple quantitative model with a saturating response curve that approximates the overall behavior of this plant-pathogen system.

Algorithms↗

PubMed2003

BRITTLE CULM1, which encodes a COBRA-like protein, affects the mechanical properties of rice plants.

Plant mechanical strength is an important agronomic trait. To understand the molecular mechanism that controls the plant mechanical strength of crops, we characterized the classic rice mutant brittle culm1 (bc1) and isolated BC1 using a map-based cloning approach. BC1, which encodes a COBRA-like protein, is expressed mainly in developing sclerenchyma cells and in vascular bundles of rice. In these types of cells, mutations in BC1 cause not only a reduction in cell wall thickness and cellulose content but also an increase in lignin level, suggesting that BC1, a gene that controls the mechanical strength of monocots, plays an important role in the biosynthesis of the cell walls of mechanical tissues.

Amino Acid Sequence↗