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Ning Su

Publications and source records attributed to Ning Su.

16 recordsLinked to original sources
PubMed2006

Fine mapping of S32(t), a new gene causing hybrid embryo sac sterility in a Chinese landrace rice (Oryza sativa L.).

Ketan Nangka, the donor of wide compatibility genes, showed sterility when crossed to Tuanguzao, a landrace rice from Yunnan province, China. Genetic and cytological analyses revealed that the semi-sterility was primarily caused by partial abortion of the embryo sac. Genome-wide analysis of the linkage map constructed from the backcross population of Tuanguzao/Ketan Nangka//Ketan Nangka identified two independent loci responsible for the hybrid sterility located on chromosomes 2 and 5, which explained 18.6 and 20.1% of phenotypic variance, respectively. The gene on chromosome 5 mapped to the previously reported sterility gene S31(t), while the gene on chromosome 2, a new hybrid sterility gene, was tentatively designated as S32(t). The BC1F2 was developed for further confirmation and fine mapping of S32(t). The gene S32(t) was precisely mapped to the same region as that detected in the BC1F1 but its position was narrowed down to an interval of about 1.9 cM between markers RM236 and RM12475. By assaying the recombinant events in the BC1F2, S32(t) was further narrowed down to a 64 kb region on the same PAC clone. Sequence analysis of this fragment revealed seven predicted open reading frames, four of which encoded known proteins and three encoded putative proteins. Further analyses showed that wide-compatibility variety Dular had neutral alleles at loci S31(t) and S32(t) that can overcome the sterilities caused by these two genes. These results are useful for map-based cloning of S32(t) and for marker-assisted transferring of the neutral allele in hybrid rice breeding.

Base Pairing↗
PubMed2006

Distinct reorganization of the genome transcription associates with organogenesis of somatic embryo, shoots, and roots in rice.

Most plant cells retain the capacity to differentiate into all the other cell and organ types that constitute a plant. However, genome-wide transcriptional activities underlying the process of cell differentiation are poorly understood, especially in monocot plants. Here we used a rice (Oryza sativa) cell culture system to generate somatic embryos, which were further induced into shoots and roots. The global transcriptional reorganization during the development of somatic embryos, shoots, and roots from cultured cells was studied using a rice whole genome microarray and verified by RNA blotting analysis of representative genes. Overall, only 1-3% of expressed genes were differentially regulated during each organogenesis process at the examined time point. Also metabolic pathways were minimally regulated. Thus the genes that dictating organ formation should be relatively small in number. Comparison of these three transcriptomes revealed little overlap during these three organogenesis processes. These results indicate that each organogenesis involves specific reorganization of genome expression.

Cells, Cultured↗
PubMed2006

[Protective effect of losartan on endothelial cells exposed to high glucose levels in vitro].

OBJECTIVE: To investigate the effect of losartan (an angiotensin II type I receptor antagonist) on endothelial cells exposed to high glucose in vitro and related mechanism. METHODS: Vascular endothelial cells of human umbilical vein were cultured in media with high glucose levels. The activities of SOD and CAT, the level of MDA were measured by spectrophotometry in the conditioned media of endothelial cells, the VEGF mRNA expression was performed using semi-quantitative reverse transcription PCR (RT-PCR) in the cell lysates, and the protein expression of VEGF was examined by enzyme-linked immunosorbent assay (ELISA) in the supernatants of cultured cells. RESULT: When endothelial cells were cultured in high glucose, the activities of SOD and CAT were significantly decreased, but the level of MDA was markedly increased. However, the high glucose-induced effects were inhibited by losartan. The application of high glucose upregulated the mRNA and protein expression of VEGF in endothelial cells, which was also attenuated by losartan. CONCLUSION: High glucose disrupts the oxidative equilibrium and increases the expression of VEGF in endothelial cells, which can be inhibited by losartan.

Angiotensin II Type 1 Receptor Blockers↗
PubMed2005

Genome-wide transcription analyses in rice using tiling microarrays.

Sequencing and computational annotation revealed several features, including high gene numbers, unusual composition of the predicted genes and a large number of genes lacking homology to known genes, that distinguish the rice (Oryza sativa) genome from that of other fully sequenced model species. We report here a full-genome transcription analysis of the indica rice subspecies using high-density oligonucleotide tiling microarrays. Our results provided expression data support for the existence of 35,970 (81.9%) annotated gene models and identified 5,464 unique transcribed intergenic regions that share similar compositional properties with the annotated exons and have significant homology to other plant proteins. Elucidating and mapping of all transcribed regions revealed an association between global transcription and cytological chromosome features, and an overall similarity of transcriptional activity between duplicated segments of the genome. Collectively, our results provide the first whole-genome transcription map useful for further understanding the rice genome.

Chromosomes↗
PubMed2005

Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture.

BACKGROUND: Sequencing and annotation of the genome of rice (Oryza sativa) have generated gene models in numbers that top all other fully sequenced species, with many lacking recognizable sequence homology to known genes. Experimental evaluation of these gene models and identification of new models will facilitate rice genome annotation and the application of this knowledge to other more complex cereal genomes. RESULTS: We report here an analysis of the chromosome 10 transcriptome of the two major rice subspecies, japonica and indica, using oligonucleotide tiling microarrays. This analysis detected expression of approximately three-quarters of the gene models without previous experimental evidence in both subspecies. Cloning and sequence analysis of the previously unsupported models suggests that the predicted gene structure of nearly half of those models needs improvement. Coupled with comparative gene model mapping, the tiling microarray analysis identified 549 new models for the japonica chromosome, representing an 18% increase in the annotated protein-coding capacity. Furthermore, an asymmetric distribution of genome elements along the chromosome was found that coincides with the cytological definition of the heterochromatin and euchromatin domains. The heterochromatin domain appears to associate with distinct chromosome level transcriptional activities under normal and stress conditions. CONCLUSION: These results demonstrated the utility of genome tiling microarray in evaluating annotated rice gene models and in identifying novel transcriptional units. The tiling microarray sanalysis further revealed a chromosome-wide transcription pattern that suggests a role for transposable element-enriched heterochromatin in shaping global transcription in response to environmental changes in rice.

Chromosomes, Plant↗
PubMed2005

A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription.

The complete genome sequence of cultivated rice (Oryza sativa) provides an unprecedented opportunity to understand the biology of this model cereal. An essential and necessary step in this effort is the determination of the coding information and expression patterns of each sequenced chromosome. Here, we report an analysis of the transcriptional activity of rice chromosome 4 using a tiling path microarray based on PCR-generated genomic DNA fragments. Six representative rice organ types were examined using this microarray to catalog the transcribed regions of rice chromosome 4 and to reveal organ- and developmental stage-specific transcription patterns. This analysis provided expression support for 82% of the gene models in the chromosome. Transcriptional activities in 1643 nonannotated regions were also detected. Comparison with cytologically defined chromatin features indicated that in juvenile-stage rice the euchromatic region is more actively transcribed than is the transposon-rich heterochromatic portion of the chromosome. Interestingly, increased transcription of transposon-related gene models in certain heterochromatic regions was observed in mature-stage rice organs and in suspension-cultured cells. These results suggest a close correlation between transcriptional activity and chromosome organization and the developmental regulation of transcription activity at the chromosome level.

Chromosome Mapping↗
PubMed2005

A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray.

As the international efforts to sequence the rice genome are completed, an immediate challenge and opportunity is to comprehensively and accurately define all transcription units in the rice genome. Here we describe a strategy of using high-density oligonucleotide tiling-path microarrays to map transcription of the japonica rice genome. In a pilot experiment to test this approach, one array representing the reverse strand of the last 11.2 Mb sequence of chromosome 10 was analyzed in detail based on a mathematical model developed in this study. Analysis of the array data detected 77% of the reference gene models in a mixture of four RNA populations. Moreover, significant transcriptional activities were found in many of the previously annotated intergenic regions. These preliminary results demonstrate the utility of genome tiling microarrays in evaluating annotated rice gene models and in identifying novel transcription units that will facilitate rice genome annotation.

Carbocyanines↗
PubMed2005

A microarray analysis of the rice transcriptome and its comparison to Arabidopsis.

Arabidopsis and rice are the only two model plants whose finished phase genome sequence has been completed. Here we report the construction of an oligomer microarray based on the presently known and predicted gene models in the rice genome. This microarray was used to analyze the transcriptional activity of the gene models in representative rice organ types. Expression of 86% of the 41,754 known and predicted gene models was detected. A significant fraction of these expressed gene models are organized into chromosomal regions, about 100 kb in length, that exhibit a coexpression pattern. Compared with similar genome-wide surveys of the Arabidopsis transcriptome, our results indicate that similar proportions of the two genomes are expressed in their corresponding organ types. A large percentage of the rice gene models that lack significant Arabidopsis homologs are expressed. Furthermore, the expression patterns of rice and Arabidopsis best-matched homologous genes in distinct functional groups indicate dramatic differences in their degree of conservation between the two species. Thus, this initial comparative analysis reveals some basic similarities and differences between the Arabidopsis and rice transcriptomes.

Arabidopsis↗
PubMed2005

Genome analysis and functional characterization of the E2 and RING-type E3 ligase ubiquitination enzymes of Arabidopsis.

Attachment of ubiquitin to substrate proteins is catalyzed by the three enzymes E1, E2 (ubiquitin conjugating [UBC]), and E3 (ubiquitin ligase). Forty-one functional proteins with a UBC domain and active-site cysteine are predicted in the Arabidopsis (Arabidopsis thaliana) genome, which includes four that are predicted or shown to function with ubiquitin-like proteins. Only nine were previously characterized biochemically as ubiquitin E2s. We obtained soluble protein for 22 of the 28 uncharacterized UBCs after expression in Escherichia coli and demonstrated that 16 function as ubiquitin E2s. Twelve, plus three previously characterized ubiquitin E2s, were also tested for the ability to catalyze ubiquitination in vitro in the presence of one of 65 really interesting new gene (RING) E3 ligases. UBC22, UBC19-20, and UBC1-6 had variable levels of E3-independent activity. Six UBCs were inactive with all RINGs tested. Closely related UBC8, 10, 11, and 28 were active with the largest number of RING E3s and with all RING types. Expression analysis was performed to determine whether E2s or E3s were expressed in specific organs or under specific environmental conditions. Closely related E2s show unique patterns of expression and most express ubiquitously. Some RING E3s are also ubiquitously expressed; however, others show organ-specific expression. Of all the organs tested, RING mRNAs are most abundant in floral organs. This study demonstrates that E2 diversity includes examples with broad and narrow specificity toward RINGs, and that most ubiquitin E2s are broadly expressed with each having a unique spatial and developmental pattern of expression.

Arabidopsis↗
PubMed2005

Modulation of F1 hybrid stature without altering parent plants through trans-activated expression of a mutated rice GAI homologue.

Hybrid breeding, by taking advantage of heterosis, brings about many superior properties to the F1 progeny. However, some properties, such as increased plant height, are not desirable for agronomic purposes. To specifically counter the height increase associated with hybrid progeny, we employed an Arabidopsis model and tested a trans-activation system for specifically expressing a mutated GAI gene only in the F1 hybrid plants to reduce plant stature. A transcriptional activator, the Gal4 DNA-binding domain fused to the acidic activation domain of herpes simplex virus VP16 protein, driven by a maize ubiquitin promoter, was introduced in one parental line. A rice GAI homologue with an N-terminal deletion of the DELLA domain, driven by a promoter that is responsive to the transcriptional activator, was transferred into another parental line. After genetic crossing, trans-activation of the GAI mutant gene resulted in a dwarf phenotype. Over 50 pair-wise crosses between the parental lines were performed, and analyses suggested that the percentage of F1 progeny exhibiting dwarfism ranged from about 25% to 100%. Furthermore, the dwarfism trait introduced in F1 progeny did not seem to affect total seed yield. Our result suggests the feasibility of manipulating F1 hybrid progeny traits without affecting parent plants or the agronomic property of the progeny.

Journal Article↗
PubMed2005

[Rapid analysis of genetically modified soybean by a duplex PCR-capillary electrophoresis system with laser-induced fluorescence detection].

OBJECTIVE: To develop a rapid detection method for genetically modified soybean resistant to glyphosate. METHODS: A duplex PCR was performed with primers designed in this study to simultaneously amplify heterogenous genes in transgenic soybean: CaMV-35S promoter, NOS terminator and CP4-EPSPS gene. And a simple capillary electrophoresis with laser-induced fluorescence detection (CE-LIF) was developed and applied to the rapid analysis of the above PCR products by using a 50 cm length x 100 microm i.d. capillary coated with linear polyacrylamide and an 8 g/L HPMC-4000 sieving buffer under 200 V/cm electric field strength. RESULTS: The proposed method was able to simultaneously detect the three heterogenous genes existing in genetically modified soybean under the optimization conditions of PCR and capillary electrophoresis. The measured sequences of the duplex PCR products were identical with the original genes' sequences. Moreover, the sample volumes required were not more than 5 nl and the detection could be completed in less than 24 min. The relative standard deviations (R. S. D.) of the migration times for the PCR products were < or = 3.2%. CONCLUSION: In comparison with agarose gels electrophoresis, the duplex PCR-based capillary electrophoretic method with laser-induced fluorescence detection is rapid, sensitive and accurate, and it is suitable for detection of genetically modified soybean.

DNA, Plant↗
PubMed2003

Foot-and-mouth disease virus VP1 protein fused with cholera toxin B subunit expressed in Chlamydomonas reinhardtii chloroplast.

A Chlamydomonas reinhardtii chloroplast expression vector, pACTBVP1, containing the fusion of the foot and mouth disease virus (FMDV) VP1 gene and the cholera toxin B subunit (CTB) gene was constructed and transfered to the chloroplast genome of C. reinhardtii by the biolistic method. The transformants were identified by PCR, Southern blot, Western blot and ELISA assays after selection on resistant medium and incubation in the dark. The CTBVP1 fusion protein was expressed in C. reinhardtii chloroplast and accounted for up to 3% of the total soluble protein. The fusion protein also retained both GM1-ganglioside binding affinity and antigenicity of the FMDV VP1 and CTB proteins. These experimental results support the possibility of using transgenic chloroplasts of green alga as a mucosal vaccine source.

Animals↗
PubMed2002

[The insect resistance of OC and Bt transplastomic plant and the phenotype of their progenies].

The Bt gene and OC gene were cotransformed to tobacco chloroplast with particle bombardment method and spectinomycin resistance tobacco seedlings were obtained. Bioassays showed that the transgenic tobacco containing both genes had enhanced toxicity to the larvae of cotton bollworm (helicoverpa zea) by comparison with the plants containing only Bt or OC gene. Southern-blotting analysis and genetic analysis of progenies showed that the Bt and OC gene expressed and was inherited maternally to the progenies.

English Abstract↗
PubMed1999

Syntheses and Metal Ion Complexation of Novel 8-Hydroxyquinoline-Containing Diaza-18-Crown-6 Ligands and Analogues.

Ten new 8-hydroxyquinoline-containing diaza-18-crown-6 ligands and analogues were synthesized via a one-pot or stepwise Mannich reaction, reductive amination, or by reacting diaza-18-crown-6 with 5,7-dichloro-2-iodomethyl-8-quinolinol in the presence of N,N-diisopropylethylamine. The Mannich reaction of N,N'-bis(methoxymethyl)diaza-18-crown-6 with 4-chloro-2-(1H-pyrazol-3-yl)phenol gave the NCH(2)N-linked bis(3-(5-chloro-2-hydroxy)pyrazol-1-ylmethyl)-substituted diazacrown ether (14) in a 98% yield. The reaction of bis(N,N'-methoxymethyldiaza)-18-crown-6 with 2.2 equiv of 10-hydroxybenzoquinoline gave only the monosubstituted diazacrown ether ligand (8). Interaction of some of the ligands with various metal ions was evaluated by a calorimetric titration technique at 25 degrees C in MeOH. Bis(8-hydroxyquinoline-2-ylmethyl)-substituted ligand 13 forms a very strong complex with Ba(2+) (log K = 11.6 in MeOH) and is highly selective for Ba(2+) over Na(+), K(+), Zn(2+), and Cu(2+) (selectivity factor > 10(6)). The (1)H NMR spectral studies of the Ba(2+) complexes with bis(8-hydroxyquinoline-2-ylmethyl)- and bis(5,7-dichloro-8-hydroxyquinoline-2-ylmethyl)-substituted diaza-18-crown-6 ligands (13 and 10) suggest that these complexes are cryptate-like structures with the two overlapping hydroxyquinoline rings forming a pseudo second macroring. UV-visible spectra of the metal ion complexes with selected ligands suggest that these ligands might be used as chromophoric or fluorophoric sensors.

Journal Article↗
PubMed1999

New Tetraazacrown Ethers Containing Two Pyridine, Quinoline, 8-Hydroxyquinoline, or 8-Aminoquinoline Sidearms.

A series of macrocyclic tetraazacrown ethers containing two pyridine, quinoline, 8-hydroxyquinoline, or 8-aminoquinoline sidearms has been prepared. Crab-like cyclization of bis(alpha-chloroacetamide)s and diamines followed by reduction of the cyclic diamides was used to synthesize the selected crown ethers containing two unsubstituted macroring nitrogen atoms. The preparation of the macrocycles with sidearms was accomplished by reductive amination of the proper aldehydes with the crown ethers using sodium triacetoxyborohydride (NaBH(OAc)(3)) as the reducing agent. The 8-hydroxyquinoline- and 8-aminoquinoline-containing macrocycles were synthesized by reductive amination of 8-acetoxyquinoline-2-carboxaldehyde or 8-nitroquinoline-2-carboxaldehyde followed by removing the acetate groups or reducing the nitro groups to amino groups, respectively. Complexation of ligand 22 with Cu(2+), Co(2+), Ni(2+), Zn(2+), Cd(2+), and Pb(2+) was evaluated potentiometrically in aqueous solution (0.10 M Me(4)NCl) at 25 degrees C. Ligand 22 formed very stable complexes with these metal ions. The UV-vis spectra of 22 and its complexes were examined in an aqueous acetic acid buffer solution (pH 5). The 22-Cu(2+) complex provided a new absorption band at 258 nm.

Journal Article↗