[Show abstract][Hide abstract] ABSTRACT: Miniature inverted repeat transposable element (MITE) is one type of transposable element (TE), which is largely found in eukaryotic genomes and involved in a wide variety of biological events. However, only few MITEs were proved to be currently active and their physiological function remains largely unknown.
We found that the amplicon discrepancy of a gene locus LOC_Os01g0420 in different rice cultivar genomes was resulted from the existence of a member of Gaijin-like MITEs (mGing). This result indicated that mGing transposition was occurred at this gene locus. By using a modified transposon display (TD) analysis, the active transpositions of mGing were detected in rice Jiahua No. 1 genome under three conditions: in seedlings germinated from the seeds received a high dose γ-ray irradiation, in plantlets regenerated from anther-derived calli and from scutellum-derived calli, and were confirmed by PCR validation and sequencing. Sequence analysis revealed that single nucleotide polymorphisms (SNPs) or short additional DNA sequences at transposition sites post mGing transposition. It suggested that sequence modification was possibly taken place during mGing transposition. Furthermore, cell re-differentiation experiment showed that active transpositions of both mGing and mPing (another well studied MITE) were identified only in regenerated plantlets.
It is for the first time that mGing active transposition was demonstrated under γ-ray irradiation or in cell re-differentiation process in rice. This newly identified active MITE will provide a foundation for further analysis of the roles of MITEs in biological process.
[Show abstract][Hide abstract] ABSTRACT: Changes in water potential, growth elongation, photosynthesis of three-leaf-old seedlings of maize inbred line YQ7-96 under water deficit (WD) for 0.5, 1 and 2 h and re-watering (RW) for 24 h were characterized. Gene expression was analyzed using cDNA microarray covering 11,855 maize unigenes. As for whole maize plant, the expression of WD-regulated genes was characterized by up-regulation. The expression of WD-regulated genes was categorized into eight different patterns, respectively, in leaves and roots. Newly found and WD-affected cellular processes were metabolic process, amino acid and derivative metabolic process and cell death. A great number of the analyzed genes were found to be regulated specifically by RW and commonly by both WD and RW, respectively, in leaves. It is therefore concluded that (1) whole maize plant tolerance to WD, as well as growth recovery from WD, depends at least in part on transcriptional coordination between leaves and roots; (2) WD exerts effects on the maize, especially on basal metabolism; (3) WD could probably affect CO(2) uptake and partitioning, and transport of fixed carbons; (4) WD could likely influence nuclear activity and genome stability; and (5) maize growth recovery from WD is likely involved in some specific signaling pathways related to RW-specific responsive genes.
Theoretical and Applied Genetics 07/2011; 123(6):943-58. · 3.66 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Effective non-invasive monitoring method to tell histopathology is a big challenge in renal transplantation.
We used 70-mer long oligonucleotide array with 449 immune related genes to determine gene expression profiles of peripheral blood mononuclear cells (PBMCs) under different immune status including stable renal function (TX), acute tubular necrosis (ATN), biopsy conformed acute rejection (AR), clinical rejection with pathology of borderline changes (BL), clinical rejection without biopsy proven/presumed rejection (PR) and renal dysfunction without rejection (NR).
Distinct molecular expression signatures in each group were found to correlate with histopathology. And we concluded that B cell chemokine CXCL13 and mast cell may play a role in renal allograft rejection through significant difference analysis and functional pathway analysis.
It provides a potential non-invasive method for monitoring renal allograft function and immune status of renal transplant recipients.
[Show abstract][Hide abstract] ABSTRACT: A cDNA library was constructed from the root tissues of cassava variety Huanan 124 at the root bulking stage. A total of 9,600 cDNA clones from the library were sequenced with single-pass from the 5'-terminus to establish a catalogue of expressed sequence tags (ESTs). Assembly of the resulting EST sequences resulted in 2,878 putative unigenes. Blastn analysis showed that 62.6% of the unigenes matched with known cassava ESTs and the rest had no 'hits' against the cassava database in the integrative PlantGDB database. Blastx analysis showed that 1,715 (59.59%) of the unigenes matched with one or more GenBank protein entries and 1,163 (40.41%) had no 'hits'. A cDNA microarray with 2,878 unigenes was developed and used to analyze gene expression profiling of Huanan 124 at key growth stages including seedling, formation of root system, root bulking, and starch maturity. Array data analysis revealed that (1) the higher ratio of up-regulated ribosome-related genes was accompanied by a high ratio of up-regulated ubiquitin, proteasome-related and protease genes in cassava roots; (2) starch formation and degradation simultaneously occur at the early stages of root development but starch degradation is declined partially due to decrease in UDP-glucose dehydrogenase activity with root maturity; (3) starch may also be synthesized in situ in roots; (4) starch synthesis, translocation, and accumulation are also associated probably with signaling pathways that parallel Wnt, LAM, TCS and ErbB signaling pathways in animals; (5) constitutive expression of stress-responsive genes may be due to the adaptation of cassava to harsh environments during long-term evolution.
[Show abstract][Hide abstract] ABSTRACT: So far, the tolerance mechanisms of plant tolerance to aluminium (Al) toxicity are still controversial. This will require an interdisciplinary approaches integrating genetic, molecular, and physiological investigations. To lay a foundation for studying mechanism of whole maize plant tolerance to Al stress (AS) and growth recovery by removal of Al toxicity (RAT), temporal physiological responses and comparative transcriptional profiling of roots and leaves of maize inbred line YQ7-96 under AS with 0.5 mmol L−1 AlCl3·6H2O and RAT were studied. In addition to toxicity towards maize, AS can lead to water deficit effect on whole maize plant. There exists independence of transcriptional response mechanisms between leaves and roots when whole maize plant responds to AS and then undergoes RAT treatment. Amino acid metabolism pathways play a very important role in Al detoxification. There exist some signaling pathways parallel to human's ones, including Wnt, ErbB, TGF-beta and Jak-STAT and the type III secretion system, which probably govern maize response to AS and RAT. The data presented in this study are very helpful to understanding of the Al-tolerant mechanisms of whole maize plant.
Environmental and Experimental Botany 01/2010; 69(2):158-166. · 3.00 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We studied the transcriptional profiles of leaves and roots of three-leaf stage seedlings of the maize inbred line YQ7-96 under conditions of salt stress (100 mM NaCl) and removal of salt stress (RSS). A total of 296 genes were regulated specifically by the stress, of which 206 were specific to leaves and 90 were specific to roots. Stress-regulated genes were classified into eight and seven expression patterns for leaves and roots, respectively. There were 60 genes which were regulated specifically by RSS, 27 of which were specific to leaves and 33 specific to roots. No genes were found to be co-regulated in tissues and to be regulated commonly by the stress and RSS. It can be concluded that (i) at the early stage of the stress, transcriptional responses are directed at water deficit in maize leaves but at both water deficit and Na+ accumulation in roots; (ii) at the later stage, the responses in leaves and roots result from dual effects of both water deficit and Na+ accumulation; (iii) the polyamine metabolic pathway is an important linker for the co-ordination between leaves and roots to accomplish the tolerance of the whole maize plant to the stress; (iv) the stress can lead to genomic restructuring and nuclear transport in maize; (v) maize leaves are distinct from roots in terms of molecular mechanisms for responses to and growth recovery from the stress; and (vi) mechanisms for the maize responses to the stress differ from those for their growth recovery during RSS.
Plant and Cell Physiology 04/2009; 50(4):889-903. · 4.98 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Appressorium is an infection structure of the phytopathogenic fungus Magnaporthe grisea. Analysis of gene expression profiles of appressorium development provides insight into the molecular basis of pathogenicity and control of this fungal plant disease. A cDNA array representing 2927 unique genes based on a large EST (expressed sequence tag) database of M. grisea strain Y34 was constructed and used to profile the gene expression patterns at mycelium and appressorium maturation stages. Compared with mycelia, 55 up-regulated and 22 down-regulated genes were identified in mature appressoria. Among 77 genes, 16 genes showed no similarity to the genome sequences of M. grisea. A novel homologue of peptidyl-prolyl cis-trans isomerase was found to be expressed at low-level in mature appressoria of M. grisea. The results indicated that the genes such as pyruvate carboxylase, phospholipid metabolism-related protein and glyceraldehyde 3-phosphate dehydrogenase involved in gluconeogenesis, lipid metabolism and glycolysis, showed differential expression in mature appressoria. Furthermore, genes such as PTH11, beta subunit of G protein and SGT1 involved in cell signalling, were expressed differentially in mature appressoria. Northern blot analysis was used to confirm the cDNA array results.
Journal of Zhejiang University SCIENCE B 03/2007; 8(2):88-97. · 1.11 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: To investigate the changes of G protein-inositol phosphates pathway-related genes and evaluate the role of such changes in the pathogenesis of essential hypertension.
The pressures of the caudal arteries and body weights of 30 spontaneous hypertensive rats (SHRs), 7 two-week-old, 7 4-week-old, 6 six-week-old, 6 eight-week-old, 6 ten-week-old, and 6 twelve-week-old, and 38 normotensive Wistar-Kyoto (WKY) rats, 6 two-week-old, 6 four-week-old, 6 six-week-old, 6 six-week-old, 6 eight-week-old, 7 ten-week-old, and 7 twelve-week-old, were measured. Then the rats were killed and their hearts, aortas, livers, and kidneys were taken out. 294 specimens of total RNA were obtained from the tissues of ventricle of heart, aortic smooth muscle, liver and kidney. RNA array was used to determine the mRNA levels of G proteins G11 and Gq, and phospholipase C-beta (PLCbeta).
The systolic blood pressures of the 6, 8, 10, and 12-week-old SHRs were 158 mm Hg +/- 8 mm Hg, 174 mm Hg +/- 4 mm Hg, 198 mm Hg +/- 13 mm Hg, and 217 mm Hg +/- 9 mm Hg respectively, all significantly higher than those of the age-matched WKY rats (109 mm Hg +/- 6 mm Hg, 128 mm Hg +/- 5 mm Hg,142 mm Hg +/- 4 mm Hg, and 141 mm Hg +/- 5 mm Hg respectively, all P <0.01). The cardiosomatic ratios of the 10- and 12-week-old SHRs were both significantly higher than those of the age-matched WKY rats (both P < 0.01). The G11 mRNA levels in the heart tissue of the 4, 6, 8, 10, and 12-week-old SHRs were 1.42 +/- 0.35, 1.87 +/- 0.40, 1.96 +/- 0.24, 2.09 +/- 0.38, and 2.34 +/- 0.45, all significantly higher than those of the age-matched WKY rats (1.05 +/- 0.18, 1.25 +/- 0.37, 1.26 +/- 0.35, 1.45 +/- 0.30, and 1.51 +/- 0.42 respectively, P < 0.05 or P < 0.01). The Gq mRNA levels of the 4, 6, 8, 10, and 12-week-old SHRs were 1.12 +/- 0.21, 1.30 +/- 0.26, 1.45 +/- 0.35, 1.77 +/- 0.42, and 2.05 +/- 0.46, respectively, all significantly higher than those of the age-matched WKY rats (0.88 +/- 0.09, 0.96 +/- 0.10, 1.03 +/- 0.10, 1.21 +/- 0.38, and 1.29 +/- 0.39 respectively, P < 0.05 or P < 0.01). Similar results were found in the G11 and Gq mRNA levels of the aorta and kidney tissues. The levels of PLCbeta expression in the heart and kidney tissues of the 4, 6, 6, 8, 10, and 12-week-old SHRs were all significantly increased (P <0.05 or P <0.01). Galpha, Gq, and PLCbeta were not significantly expressed in the liver. PLCbeta was hardly found in the aorta.
Increase of the expression of G protein-inositol phosphates pathway-related genes is an important molecular biological mechanism in the pathogenesis and development of essential hypertension.
[Show abstract][Hide abstract] ABSTRACT: AN EXPRESSED SEQUENCE TAGS (EST) resource for tobacco plants (Nicotiana tabacum) was established using high-throughput sequencing of randomly selected clones from 1 cDNA library representing a range of plant organs (leaf, stem, root and root base). Over 5000 ESTs were generated from the 3'-ends of 8000 clones, analyzed by BLAST searches, and categorized functionally. Clustering of these ESTs identified a unigene set of 3600 genes that are represented in the EST collection. 696 unique sequences (19.33% in TUTs) were identified as highly significant matches (E≤10 -20) to the known gene sequences and were regarded as representation of known genes according to results from the BLASTX research of the available database. All annotation ESTs were classified in 18 functional categories, with unique transcripts involved in energy the largest group accounting for 32.32% in all annotation ESTs. After excluding 2450 non-significant TUTs in sequence similarity, 100 unique sequences (1.67% in total TUTs) were identified from N. tabacum database and the remaining 1050 TUTs showed partial homology to genes in other organisms. Through comparing the hybridization data, 359 high-quality ESTs from four tobacco varieties were generated and analyzed using the Cyber-T statistic program, 7 EST from this analysis may have a relation to TMV resistance in tobacco plants, particularly to the Hongda variety. The array results were confirmed using a Real-time quantitative RT-PCR.
[Show abstract][Hide abstract] ABSTRACT: To evaluate the expression of nitric oxide synthase III (NOS III) mRNA in the heart, aorta, kidney and liver of spontaneously hypertensive rats (SHR).
Two hundred and ninety-four total RNA samples were obtained from the tissues of ventricle, aortic smooth muscle, kidney and liver of SHR and normotensive rats (Wistar-Kyoto rats, WKY). RNA array was used to determine the mRNA levels of NOS III of the two groups.
Compared with WKY, the systolic blood pressure increased significantly in SHR at 6-week-old, 8-week-old, 10-week-old and 12-week-old [(158.50 +/-7.69 vs 108.67 +/-5.89) mmHg, (174.33 +/-4.46 vs 128.50 +/-4.97) mmHg, (198.00 +/-13.45 vs 142.00 +/-3.58) mmHg, (216.67 +/-8.91 vs 141.17 +/-4.92) mmHg, P<0.01], and the ventricle/body weight ratio was significant higher at 10-week-old and 12-week-old [(4.08 +/-0.17 vs 3.59 +/-0.11, 4.05 +/-0.18 vs 3.40 +/-0.19)mg/g, P<0.01]. In the heart tissue and the kidney, the mRNA levels of NOS III were significantly increased at 6-week-old, 8-week-old, 10-week-old and 12-week-old (1.12 +/-0.18 vs 0.90 +/- 0.15, 1.46 +/- 0.34 vs 1.06 +/-0.18, 1.66 +/- 0.31 vs 1.21 +/- 0.30, 1.98 +/- 0.40 vs 1.31 +/-0.38, P <0.05) and at 4-week-old, 6-week-old, 8-week-old, 10-week-old and 12-week-old (1.10 +/- 0.21 vs 0.81 +/-0.11, 1.28 +/-0.18 vs 0.95 +/-0.13,1.31 +/-0.23 vs 0.99 +/-0.23, 1.70 +/-0.30 vs 1.08 +/-0.25, 1.83 +/-0.33 vs 1.15 +/-0.20, P<0.05 or P<0.01), respectively. There was no significant difference of the NOS III expression in the liver and no significant signals were detected in the aortic smooth muscle.
The results provide the evidence of the increased expression of NOS III in different tissues in SHR and suggests the progressive nature of essential hypertension.
Zhejiang da xue xue bao. Yi xue ban = Journal of Zhejiang University. Medical sciences 10/2004; 33(5):443-8.
[Show abstract][Hide abstract] ABSTRACT: A pair of near isogenic lines G205 and G71 were selected from recombinant inbred lines (RIL) of Zhong156 x Gumei2. On the resistance locus Pi-25(t), G205 had the resistant allele that was from Gumei 2 while G71 had the susceptible allele that was from Zhong156. For the genetic background, different alleles were detected on only 24 loci out of the 672 RFLP or SSLP loci surveyed. The expression profiles of G205 and G71 in response to Magnaporthe grisea were investigated using cDNA microarray containing 2200 Expression Sequence Tags (ESTs). The leaves were inoculated with the pathogen for 12 hours at 4-leaf stage and 998 genes were identified in total. Three genes were up-regulated significantly by the fungus in G205 only. The functions of two genes were known but that of the third gene were unknown. The two genes encoded casein kinase II alpha subunit and retrotransponson TOS17 insertion element respectively. Other thirty-five genes had similar expression patterns between NILs. Among them, 17 genes were up-regulated while 18 genes were down-regulated by the inoculation. The functions of 33 out of the 35 genes were known. BLAST analysis showed that all thirty-five. BLAST analysis showed that all thirty-five genes with known functions were relative to defense reactions, signal transduction, stress response, photosynthesis and sugar metabolism. Northern blot confirmed that four of five differentially displayed genes randomly selected had the same expression patterns as those detected in cDNA microarray. Two of them were up-regulated genes encoding casein kinase II alpha subunit and glycine-rich protein (Grp), and the other two down-regulated genes encoding nitrilase-associated protein and 18S small subnit ribosomal RNA gene respectively. Northern blot also revealed that the expression of Grp was consistently up-regulated from 0 to 36 h after the inoculation of the fungus. These results showed that cDNA microarray was a useful tool to study the molecular mechanisms of disease resistance in plants.