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1.  Quantitative phosphoproteomic profiling of fiber differentiation and initiation in a fiberless mutant of cotton 
BMC Genomics  2014;15(1):466.
The cotton (Gossypium spp.) fiber cell is an important unicellular model for studying cell differentiation. There is evidence suggesting that phosphorylation is a critical post-translational modification involved in regulation of a wide range of cell activities. Nevertheless, the sites of phosphorylation in G. hirsutum and their regulatory roles in fiber cell initiation are largely unknown. In this study, we employed a mass spectrometry-based phosphoproteomics to conduct a global and site-specific phosphoproteome profiling between ovules of a fuzzless-lintless (fl) Upland cotton (G. hirsutum) mutant and its isogenic parental wild type (WT) at -3 and 0 days post-anthesis (DPA).
A total of 830 phosphopeptides and 1,592 phosphorylation sites from 619 phosphoproteins were identified by iTRAQ (isobaric tags for relative and absolute quantitation). Of these, 76 phosphoproteins and 1,100 phosphorylation sites were identified for the first time after searching the P3DB public database using the BLAST program. Among the detected phosphopeptides, 69 were differentially expressed between the fl mutant and its WT in ovules at -3 and 0 DPA. An analysis using the Motif-X program uncovered 19 phosphorylation motifs, 8 of which were unique to cotton. A further metabolic pathway analysis revealed that the differentially phosphorylated proteins were involved in signal transduction, protein modification, carbohydrate metabolic processes, and cell cycle and cell proliferation.
Our phosphoproteomics-based research provides the first global overview of phosphorylation during cotton fiber initiation, and also offers a helpful dataset for elucidation of signaling networks in fiber development of G. hirsutum.
Electronic supplementary material
The online version of this article (doi: 10.1186/1471-2164-15-466) contains supplementary material, which is available to authorized users.
PMCID: PMC4070576  PMID: 24923550
Gossypium hirsutum; Fuzzless-lintless mutant; Fiber initiation; Phosphoproteomics
2.  Root Interactions in a Maize/Soybean Intercropping System Control Soybean Soil-Borne Disease, Red Crown Rot 
PLoS ONE  2014;9(5):e95031.
Within-field multiple crop species intercropping is well documented and used for disease control, but the underlying mechanisms are still unclear. As roots are the primary organ for perceiving signals in the soil from neighboring plants, root behavior may play an important role in soil-borne disease control.
Principal Findings
In two years of field experiments, maize/soybean intercropping suppressed the occurrence of soybean red crown rot, a severe soil-borne disease caused by Cylindrocladium parasiticum (C. parasiticum). The suppressive effects decreased with increasing distance between intercropped plants under both low P and high P supply, suggesting that root interactions play a significant role independent of nutrient status. Further detailed quantitative studies revealed that the diversity and intensity of root interactions altered the expression of important soybean PR genes, as well as, the activity of corresponding enzymes in both P treatments. Furthermore, 5 phenolic acids were detected in root exudates of maize/soybean intercropped plants. Among these phenolic acids, cinnamic acid was released in significantly greater concentrations when intercropped maize with soybean compared to either crop grown in monoculture, and this spike in cinnamic acid was found dramatically constrain C. parasiticum growth in vitro.
To the best of our knowledge, this study is the first report to demonstrate that intercropping with maize can promote resistance in soybean to red crown rot in a root-dependent manner. This supports the point that intercropping may be an efficient ecological strategy to control soil-borne plant disease and should be incorporated in sustainable agricultural management practices.
PMCID: PMC4014482  PMID: 24810161
3.  A Polymorphism of ORAI1 rs7135617, Is Associated with Susceptibility to Rheumatoid Arthritis 
Mediators of Inflammation  2014;2014:834831.
Rheumatoid arthritis (RA), a chronic inflammatory disease usually occurring in synovial tissues and joints, is highly associated with genetic and environmental factors. ORAI1, a gene related to cellular immune system, has been shown to be involved in the pathogenesis of chronic inflammatory diseases and immune diseases. To identify whether ORAI1 gene contributes to RA susceptibility, we enrolled 400 patients with RA and 621 healthy individuals for a case-control genetic association study. Five tagging single nucleotides polymorphisms (tSPNs) within ORAI1 gene were selected for genotyping. An SNP, rs7135617, showed a significant correlation with the risk of RA. Our results indicated that genetic polymorphism of ORAI1 gene is involved in the susceptibility of RA in a Taiwanese population.
PMCID: PMC3997980  PMID: 24808640
4.  Multidrug Resistance 1 Gene Variants, Pesticide Exposure, and Increased Risk of DNA Damage 
BioMed Research International  2014;2014:965729.
The P-glycoprotein, encoded by the multidrug resistance (MDR)1 gene, extrudes fat-soluble compounds to the extracellular environment. However, the DNA damage of pesticides in subjects with genetic variation in MDR1 has not been investigated. In this study, the comet assay was applied to examine the extent of DNA damage in the peripheral blood of 195 fruit growers who had been exposed to pesticides and 141 unexposed controls. The MDR1 polymorphisms were identified. Questionnaires were administered to obtain demographic data and occupational history. Results showed subjects experiencing high (2.14 μm/cell, P < 0.01) or low pesticide exposure (2.18 μm/cell, P < 0.01) had a significantly greater DNA tail moment than controls (1.28 μm/cell). Compared to the MDR1 T-129C (rs3213619) TC/CC carriers, the TT carriers had increased DNA tail moment in controls (1.30 versus 1.12 μm/cell, P < 0.01). Similar results were observed in the high and low pesticide-exposed groups. Combined analysis revealed that pesticide-exposed fruit growers with MDR1 -129 TT genotype had the greatest DNA damage in the subjects with the combinations of pesticide exposure and MDR1 -129 genotypes. In conclusion, pesticide exposed individuals with susceptible MDR1 -129 genotypes may experience increased risk of DNA damage.
PMCID: PMC3984798  PMID: 24791009
5.  Low Molecular Weight Hyaluronan Induces Lymphangiogenesis through LYVE-1-Mediated Signaling Pathways 
PLoS ONE  2014;9(3):e92857.
Hyaluronan (HA), a large nonsulfated glycosaminogycan in the extracellular matrix, whose degraded fragments termed as low molecular weight hyaluronan (LMW-HA), has been reported as an important regulator of angiogenesis. However, little is known about the influence of LMW-HA on lymphangiogenesis. In this study, we try to explore the in vitro effects of LMW-HA on lymphangiogenesis and identify the underlying molecular mechanisms. Our results showed that LMW-HA stimulation significantly increased lymphatic endothelial cells (LECs) proliferation, migration and tube formation. Further experiments demonstrated that LMW-HA altered actin cytoskeleton rearrangement and increased the formation of intense stress fibers, lamellipodia and filopodia. Mechanistically, LMW-HA stimulation resulted in rapid tyrosine phosphorylation of protein kinase C α/βII (PKCα/βII) and extracellular-regulated kinase 1/2 (ERK1/2). Lymphalic vessel endotheilial hyaluronan receptor 1 (LYVE-1), a homologue of CD44, is the main cell surface receptor for HA in LECs. Blocking the binding interaction of LMW-HA with LYVE-1 using neutralizing anti-LYVE-1 antibodies significantly inhibited LECs proliferation, migration, tube formation and signal transduction induced by LMW-HA, suggesting that LMW-HA may play a critical role in the processes required for lymphangiogenesis through interactions with its receptor LYVE-1 and triggering intracellular signal cascades.
PMCID: PMC3965470  PMID: 24667755
6.  Resveratrol Prevention of Diabetic Nephropathy Is Associated with the Suppression of Renal Inflammation and Mesangial Cell Proliferation: Possible Roles of Akt/NF-κB Pathway 
The present study was to investigate the protection of resveratrol (RSV) in diabetes associated with kidney inflammation and cell proliferation. Rat mesangial cell and streptozotocin-induced type 1 diabetes mouse model were used. In vitro, RSV attenuated high glucose-induced plasminogen activator inhibitor (PAI-1) expression and mesangial cell proliferation, as well as Akt and nuclear factor-kappa B (NF-κB) activation. The similar results were recaptured in the experiment with Akt inhibitors. In vivo, mice were divided into three groups: control group, diabetes mellitus (DM) group, and RSV-treated DM group. Compared with control group, the kidney weight to body weight ratio and albumin to creatinine ratio were increased in DM group, but not in RSV-treated DM group. Furthermore, the increased expression of PAI-1 and intercellular adhesion molecule-1 in diabetic renal cortex were also reduced by RSV administration. Besides, the kidney p-Akt/Akt ratio and NF-κB were significantly increased in DM group; however, these changes were reversed in RSV-treated DM group. Additionally, immunohistochemistry results indicated that RSV treatment reduced the density of proliferating cell nuclear antigen-positive cells significantly in glomeruli of diabetic mice. These results suggest that RSV prevents diabetes-induced renal inflammation and mesangial cell proliferation possibly through Akt/NF-κB pathway inhibition.
PMCID: PMC3941586  PMID: 24672545
7.  Close Correlation between Season of Birth and the Prevalence of Bronchial Asthma in a Taiwanese Population 
PLoS ONE  2013;8(11):e80285.
Bronchial asthma (BA), atopic dermatitis (AD), and allergic rhinitis (AR) are common allergic diseases. Environmental factors were indicated to influence the development of allergic diseases.
To evaluate the correlation between the month of birth and the prevalence of allergic diseases in Taiwan.
Data from 104,455 children were collected from the National Insurance Research Database of Taiwan. Subjects were identified by at least two service claims for ambulatory care or one claim for inpatient care. All of the enrolled patients were aged 7∼15 years in 2010. In a bio-clinical data analysis, total immunoglobulin E (IgE) and ImmunoCAP™ allergen data (CAP) from mothers and infants were collected in a medical center in Taiwan. Correlations between children's allergic factors and the season of birth were assessed.
A significant difference in the prevalence of BA according to the month of birth (Χ2 = 18.2, p<0.001) was found in the Taiwanese population. The fewest schoolchildren with were born in May (7.21%), and the most were born in October (10.59%). However, no tendency for the prevalence of AD (Χ2 = 4.6, P = 0.204) or AR (Χ2 = 4.3 P = 0.229) was found. In addition, we found that children born in autumn (August to October) had a higher prevalence of BA compared to those born in spring (February to April) (odds ratio: 1.13; 95% confidence interval: 1.05∼1.21). In a bio-clinical data study, markers of maternal and childhood allergies including IgE and CAP were detected in a risk analysis section. Children who were born in autumn had higher levels of CAP and total IgE.
The findings of this study showed that the month of birth was closely correlated with the prevalence of BA and higher levels of CAP and IgE.
PMCID: PMC3835889  PMID: 24278271
8.  Serum β-Catenin Levels Associated with the Ratio of RANKL/OPG in Patients with Postmenopausal Osteoporosis 
Objective. To demonstrate the role of Wnt/β-catenin canonical pathway in postmenopausal osteoporosis by evaluating serum β-catenin levels in patients with postmenopausal osteoporosis and analyzing their possible relationship with serum OPG, RANKL, the ratio of RANKL/OPG, sclerostin, and bone turnover markers. Methods. 480 patients with postmenopausal osteoporosis and 170 healthy postmenopausal women were enrolled in the study. Serum β-catenin, OPG, RANKL, and sclerostin levels were measured by enzyme-linked immunosorbent assay. Bone status was assessed by measuring bone mineral density and bone turnover markers. Estradiol levels were also detected. Results. Serum β-catenin levels were lower in postmenopausal osteoporotic women compared to nonosteoporotic postmenopausal women (26.26 ± 14.81 versus 39.33 ± 5.47 pg/mL, P < 0.001). Serum β-catenin was positively correlated with osteoprotegerin (r = 0.232, P < 0.001) and negatively correlated with the ratio of RANKL/OPG, body mass index, and sclerostin (r = −0.128, P = 0.005; r = −0.117, P = 0.010; r = −0.400, P < 0.001, resp.) in patients with postmenopausal osteoporosis. Conclusion. The results indicate that lower serum β-catenin and concomitantly higher ratio of RANKL/OPG may be involved in the pathogenesis of postmenopausal osteoporosis. Functional communication between RANKL/RANK/OPG system and Wnt pathways plays an important role in postmenopausal osteoporosis.
PMCID: PMC3654357  PMID: 23710175
9.  Comparative expression profiling of miRNA during anther development in genetic male sterile and wild type cotton 
BMC Plant Biology  2013;13:66.
Genetic male sterility (GMS) in cotton (Gossypium hirsutum) plays an important role in the utilization of hybrid vigor. However, the molecular mechanism of the GMS is still unclear. While numerous studies have demonstrated that microRNAs (miRNA) regulate flower and anther development, whether different small RNA regulations exist in GMS and its wild type is unclear. A deep sequencing approach was used to investigate the global expression and complexity of small RNAs during cotton anther development in this study.
Three small RNA libraries were constructed from the anthers of three development stages each from fertile wild type (WT) and its GMS mutant cotton, resulting in nearly 80 million sequence reads. The total number of miRNAs and short interfering RNAs in the three WT libraries was significantly greater than that in the corresponding three mutant libraries. Sixteen conserved miRNA families were identified, four of which comprised the vast majority of the expressed miRNAs during anther development. In addition, six conserved miRNA families were significantly differentially expressed during anther development between the GMS mutant and its WT.
The present study is the first to deep sequence the small RNA population in G. hirsutum GMS mutant and its WT anthers. Our results reveal that the small RNA regulations in cotton GMS mutant anther development are distinct from those of the WT. Further results indicated that the differently expressed miRNAs regulated transcripts that were distinctly involved in anther development. Identification of a different set of miRNAs between the cotton GMS mutant and its WT will facilitate our understanding of the molecular mechanisms for male sterility.
PMCID: PMC3639194  PMID: 23597285
10.  Repressing malic enzyme 1 redirects glucose metabolism, unbalances the redox state, and attenuates migratory and invasive abilities in nasopharyngeal carcinoma cell lines 
Chinese Journal of Cancer  2012;31(11):519-531.
A large amount of nicotinamide adenine dinucleotide phosphate (NADPH) is required for fatty acid synthesis and maintenance of the redox state in cancer cells. Malic enzyme 1 (ME1)-dependent NADPH production is one of the three pathways that contribute to the formation of the cytosolic NADPH pool. ME1 is generally considered to be overexpressed in cancer cells to meet the high demand for increased de novo fatty acid synthesis. In the present study, we found that glucose induced higher ME1 activity and that repressing ME1 had a profound impact on glucose metabolism of nasopharyngeal carcinoma (NPC) cells. High incorporation of glucose and an enhancement of the pentose phosphate pathway were observed in ME1-repressed cells. However, there were no obvious changes in the other two pathways for glucose metabolism: glycolysis and oxidative phosphorylation. Interestingly, NADPH was decreased under low-glucose condition in ME1-repressed cells relative to wild-type cells, whereas no significant difference was observed under high-glucose condition. ME1-repressed cells had significantly decreased tolerance to low-glucose condition. Moreover, NADPH produced by ME1 was not only important for fatty acid synthesis but also essential for maintenance of the intracellular redox state and the protection of cells from oxidative stress. Furthermore, diminished migration and invasion were observed in ME1-repressed cells due to a reduced level of Snail protein. Collectively, these results suggest an essential role for ME1 in the production of cytosolic NADPH and maintenance of migratory and invasive abilities of NPC cells.
PMCID: PMC3777517  PMID: 23114090
Nasopharyngeal carcinoma; malic enzyme 1; low glucose; NADPH
11.  Co-Inoculation with Rhizobia and AMF Inhibited Soybean Red Crown Rot: From Field Study to Plant Defense-Related Gene Expression Analysis 
PLoS ONE  2012;7(3):e33977.
Soybean red crown rot is a major soil-borne disease all over the world, which severely affects soybean production. Efficient and sustainable methods are strongly desired to control the soil-borne diseases.
Principal Findings
We firstly investigated the disease incidence and index of soybean red crown rot under different phosphorus (P) additions in field and found that the natural inoculation of rhizobia and arbuscular mycorrhizal fungi (AMF) could affect soybean red crown rot, particularly without P addition. Further studies in sand culture experiments showed that inoculation with rhizobia or AMF significantly decreased severity and incidence of soybean red crown rot, especially for co-inoculation with rhizobia and AMF at low P. The root colony forming unit (CFU) decreased over 50% when inoculated by rhizobia and/or AMF at low P. However, P addition only enhanced CFU when inoculated with AMF. Furthermore, root exudates of soybean inoculated with rhizobia and/or AMF significantly inhibited pathogen growth and reproduction. Quantitative RT-PCR results indicated that the transcripts of the most tested pathogen defense-related (PR) genes in roots were significantly increased by rhizobium and/or AMF inoculation. Among them, PR2, PR3, PR4 and PR10 reached the highest level with co-inoculation of rhizobium and AMF.
Our results indicated that inoculation with rhizobia and AMF could directly inhibit pathogen growth and reproduction, and activate the plant overall defense system through increasing PR gene expressions. Combined with optimal P fertilization, inoculation with rhizobia and AMF could be considered as an efficient method to control soybean red crown rot in acid soils.
PMCID: PMC3307780  PMID: 22442737
12.  catena-Poly[[(isoquinoline-κN)(triphenylphospane-κP)copper(I)]-μ-thio­cyanato-κ2 N:S] 
In the title coordination compound, [Cu(NCS)(C9H7N)(C18H15P)]n, the CuI atom is tetra­hedrally coordinated by one N atom from an isoquinoline ligand, one P atom from a triphenyl­phospane ligand, and one N and one S atom from two thio­cyanate anions. The thio­cyanide anions bridge the CuI atoms into a chain along [100]. π–π inter­actions between the pyridine and benzene rings of the isoquinoline ligands connect the chains [centroid-to-centroid distance = 3.722 (3) Å].
PMCID: PMC3297240  PMID: 22412430
13.  5,6-Dimethyl-1,2,4-triazin-3-amine 
In the crystal structure of the title compound, C5H8N4, adjacent mol­ecules are connected through N—H⋯N hydrogen bonds, resulting in a zigzag chain along [100]. The amino groups and heterocyclic N atoms are involved in further N—H⋯N hydrogen bonds, forming R 2 2(8) motifs.
PMCID: PMC3254400  PMID: 22259542
14.  Characterization of SARS-CoV-specific memory T cells from recovered individuals 4 years after infection 
Archives of virology  2009;154(7):1093-1099.
SARS-CoV infection of human results in antigen-specific cellular and humoral immune responses. However, it is critical to determine whether SARS-CoV-specific memory T cells can persist for long periods of time. In this study, we analyzed the cellular immune response from 21 SARS-recovered individuals who had been diagnosed with SARS in 2003 by using ELISA, CBA, ELISpot and multiparameter flow cytometry assays. Our results demonstrated that low levels of specific memory T cell responses to SARS-CoV S, M, E and N peptides were detected in a proportion of SARS-recovered patients, and IFN-γ was the predominant cytokine produced by T cells after stimulation with peptides. Cytometry analysis indicated that the majority of memory CD8+ T cells produced IFN-γ, whereas memory CD4+ T cells produced IFN-γ, IL-2 or TNF-α. These results might provide valuable information on the cellular immune response in recovered SARS-CoV patients for the rational design of vaccines against SARS-CoV infection.
PMCID: PMC2796960  PMID: 19526193
15.  Theoretical Study for High-Energy-Density Compounds Derived from Cyclophosphazene. IV. DFT Studies on 1,1-Diamino-3,3,5,5,7,7-hexaazidocyclotetraphosphazene and Its Isomers 
In the present study, a theoretical study of 1,1-diaminohexaazidocyclotetraphophazene (DAHA) and its isomers has been performed, using quantum computational density functional theory (B3LYP and B3PW91 methods) with 6-31G* and 6-31G** basis sets implemented in Gaussian 03 program suite. Molecular structure and bonding, vibrational frequencies, Milliken population analysis, and natural bond orbit (NBO) have been studied. The heats of formation from atomization energies have also been calculated based on the optimized geometry. The obtained heats of formation data are compared with their homologous cyclophosphazene in order to demonstrate the accuracy of the methods, which indicate that the studied compounds might be potentially used as high energetic materials. In addition, the relative stability of five isomers have been deduced based on the total energy and the gap of frontier orbital energies.
PMCID: PMC2741615  PMID: 19756156
density functional theory; vibrational analysis; Mulliken analysis; heats of formation; diamino-hexaazidocyclotetraphophazene
16.  Influence of temperature fluctuation on thermophilic anaerobic digestion of municipal organic solid waste*  
A laboratory-scale experiment was carried out to assess the influence of temperature fluctuation on thermophilic anaerobic digestion of municipal organic solid waste (MOSW). Heating failure was simulated by decreasing temperature suddenly from 55 °C to 20 °C suddenly; 2 h time is needed for temperature decrease and recovery. Under the conditions of 8.0 g/(L·d) and 15 d respectively for MOSW load and retention time, following results were noted: (1) biogas production almost stopped and VFA (volatile fatty acid) accumulated rapidly, accompanied by pH decrease; (2) with low temperature (20 °C) duration of 1, 5, 12 and 24 h, it took 3, 11, 56 and 72 h for the thermophilic anaerobic digestion system to reproduce methane after temperature fluctuation; (3) the longer the low temperature interval lasted, the more the methanogenic bacteria would decay; hydrolysis, acidification and methanogenesis were all influenced by temperature fluctuation; (4) the thermophilic microorganisms were highly resilient to temperature fluctuation.
PMCID: PMC1419061  PMID: 16502503
Temperature fluctuation; Low temperature duration; Thermophilic anaerobic digestion; Municipal organic solid waste
17.  High-density lipoprotein as a potential carrier for delivery of a lipophilic antitumoral drug into hepatoma cells 
AIM: To investigate the possibility of recombinant high-density lipoprotein (rHDL) being a carrier for delivering antitumoral drug to hepatoma cells.
METHODS: Recombinant complex of HDL and aclacinomycin (rHDL-ACM) was prepared by cosonication of apoproteins from HDL (Apo HDL) and ACM as well as phosphatidylcholine. Characteristics of the rHDL-ACM were elucidated by electrophoretic mobility, including the size of particles, morphology and entrapment efficiency. Binding activity of rHDL-ACM to human hepatoma cells was determined by competition assay in the presence of excess native HDL. The cytotoxicity of rHDL-ACM was assessed by MTT method.
RESULTS: The density range of rHDL-ACM was 1.063-1.210 g/mL, and the same as that of native HDL. The purity of all rHDL-ACM preparations was more than 92%. Encapsulated efficiencies of rHDL-ACM were more than 90%. rHDL-ACM particles were typical sphere model of lipoproteins and heterogeneous in particle size. The average diameter was 31.26±5.62 nm by measure of 110 rHDL-ACM particles in the range of diameter of lipoproteins. rHDL-ACM could bind on SMMC-7721 cells, and such binding could be competed against in the presence of excess native HDL. rHDL-ACM had same binding capacity as native HDL. The cellular uptake of rHDL-ACM by SMMC-7721 hepatoma cells was significantly higher than that of free ACM at the concentration range of 0.5-10 µg/mL (P<0.01). Cytotoxicity of rHDL-ACM to SMMC-7721 cells was significantly higher than that of free ACM at concentration range of less than 5 µg/mL (P<0.01) and IC50 of rHDL-ACM was lower than IC50 of free ACM (1.68 nmol/L vs 3 nmol/L). Compared to L02 hepatocytes, a normal liver cell line, the cellular uptake of rHDL-ACM by SMMC-7721 cells was significantly higher (P<0.01) and in a dose-dependent manner at the concentration range of 0.5-10 μg/mL. Cytotoxicity of the rHDL-ACM to SMMC-7721 cells was significantly higher than that to L02 cells at concentration range of 1-7.5 μg/mL (P<0.01). IC50 for SMMC-7721 cells (1.68 nmol/L) was lower than that for L02 cells (5.68 nmol/L), showing a preferential cytotoxicity of rHDL-ACM for SMMC-7721 cells.
CONCLUSION: rHDL-ACM complex keeps the basic physical and biological binding properties of native HDL and shows a preferential cytotoxicity for SMMC-7721 hepatoma to normal L02 hepatocytes. HDL is a potential carrier for delivering lipophilic antitumoral drug to hepatoma cells.
PMCID: PMC4250784  PMID: 15742395
High-density lipoprotein; Carrier; Antitumoral drug; SMMC-7721 hepatoma cell

Results 1-17 (17)