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1.  Spectrally Shaped DP-16QAM Super-Channel Transmission with Multi-Channel Digital Back-Propagation 
Scientific Reports  2015;5:8214.
The achievable transmission capacity of conventional optical fibre communication systems is limited by nonlinear distortions due to the Kerr effect and the difficulty in modulating the optical field to effectively use the available fibre bandwidth. In order to achieve a high information spectral density (ISD), while simultaneously maintaining transmission reach, multi-channel fibre nonlinearity compensation and spectrally efficient data encoding must be utilised. In this work, we use a single coherent super-receiver to simultaneously receive a DP-16QAM super-channel, consisting of seven spectrally shaped 10GBd sub-carriers spaced at the Nyquist frequency. Effective nonlinearity mitigation is achieved using multi-channel digital back-propagation (MC-DBP) and this technique is combined with an optimised forward error correction implementation to demonstrate a record gain in transmission reach of 85%; increasing the maximum transmission distance from 3190 km to 5890 km, with an ISD of 6.60 b/s/Hz. In addition, this report outlines for the first time, the sensitivity of MC-DBP gain to linear transmission line impairments and defines a trade-off between performance and complexity.
doi:10.1038/srep08214
PMCID: PMC4314642  PMID: 25645457
2.  Novel Three-Component Rieske Non-Heme Iron Oxygenase System Catalyzing the N-Dealkylation of Chloroacetanilide Herbicides in Sphingomonads DC-6 and DC-2 
Applied and Environmental Microbiology  2014;80(16):5078-5085.
Sphingomonads DC-6 and DC-2 degrade the chloroacetanilide herbicides alachlor, acetochlor, and butachlor via N-dealkylation. In this study, we report a three-component Rieske non-heme iron oxygenase (RHO) system catalyzing the N-dealkylation of these herbicides. The oxygenase component gene cndA is located in a transposable element that is highly conserved in the two strains. CndA shares 24 to 42% amino acid sequence identities with the oxygenase components of some RHOs that catalyze N- or O-demethylation. Two putative [2Fe-2S] ferredoxin genes and one glutathione reductase (GR)-type reductase gene were retrieved from the genome of each strain. These genes were not located in the immediate vicinity of cndA. The four ferredoxins share 64 to 72% amino acid sequence identities to the ferredoxin component of dicamba O-demethylase (DMO), and the two reductases share 62 to 65% amino acid sequence identities to the reductase component of DMO. cndA, the four ferredoxin genes, and the two reductases genes were expressed in Escherichia coli, and the recombinant proteins were purified using Ni-affinity chromatography. The individual components or the components in pairs displayed no activity; the enzyme mixture showed N-dealkylase activities toward alachlor, acetochlor, and butachlor only when CndA-His6 was combined with one of the four ferredoxins and one of the two reductases, suggesting that the enzyme consists of three components, a homo-oligomer oxygenase, a [2Fe-2S] ferredoxin, and a GR-type reductase, and CndA has a low specificity for the electron transport component (ETC). The N-dealkylase utilizes NADH, but not NADPH, as the electron donor.
doi:10.1128/AEM.00659-14
PMCID: PMC4135782  PMID: 24928877
3.  Effects of Adult Male Circumcision on Premature Ejaculation: Results from a Prospective Study in China 
BioMed Research International  2015;2015:417846.
The purpose of this study is to investigate the effects of adult male circumcision on premature ejaculation (PE). Therefore, between December 2009 and March 2014, a total of 575 circumcised men and 623 uncircumcised men (control group) were evaluated. Detailed evaluations (including circumcision and control groups) on PE were conducted before circumcision and at the 3-, 6-, 9-, and 12-month follow-up visits after circumcision. Self-estimated intravaginal ejaculatory latency time (IELT), Patient-Reported Outcome measures, and 5-item version of the International Index of Erectile Function were used to measure the ejaculatory and erectile function for all subjects. The results showed that, during the one-year follow-up, men after circumcision experienced higher IELT and better scores of control over ejaculation, satisfaction with sexual intercourse, and severity of PE than men before circumcision (P < 0.001 for all). Similarly, when compared with the control group, the circumcised men reported significantly improved IELT, control over ejaculation, and satisfaction with sexual intercourse (P < 0.001 for all). These findings suggested that circumcision might have positive effects on IELT, ejaculatory control, sexual satisfaction, and PE severity. In addition, circumcision was significantly associated with the development of PE.
doi:10.1155/2015/417846
PMCID: PMC4324807
4.  Overexpression of membrane-type 2 matrix metalloproteinase induced by hypoxia-inducible factor-1α in pancreatic cancer: Implications for tumor progression and prognosis 
Molecular and Clinical Oncology  2014;2(6):973-981.
Membrane-type 2 matrix metalloproteinase (MT2-MMP) has been identified as a powerful modulator of the pericellular environment that promotes tumor invasion and metastasis. In this study, we investigated the association of MT2-MMP and hypoxia-inducible factor-1α (HIF-1α) expression in pancreatic cancer with regard to their clinical prognostic significance. Of the tissue specimens obtained from the 78 patients included in this study, 46 (59%) were found to be positive for MT2-MMP immunostaining and MT2-MMP expression was colocalized with HIF-1α in pancreatic cancer. Using the Spearman’s rank analysis, the protein and mRNA expression level of MT2-MMP was found to be significantly correlated with HIF-1α and CD34-microvascular density in pancreatic cancer. Furthermore, the expression of MT2-MMP in response to hypoxia was increased in a time-dependent manner and the promoter luciferase reporter revealed upregulation of MT2-MMP expression induced by HIF-1α in pancreatic cancer cells. Moreover, the Cox regression model indicated that MT2-MMP was an independent prognostic factor in patients with pancreatic cancer. Our results demonstrated that the overexpression of MT2-MMP was induced by HIF-1α in response to hypoxia and was an independent prognostic factor for pancreatic cancer progression.
doi:10.3892/mco.2014.357
PMCID: PMC4179790  PMID: 25279184
membrane-type 2 matrix metalloproteinase; pancreatic cancer; hypoxia-inducible factor-1α; tumor progression; prognosis
5.  H2O2 mediates the crosstalk of brassinosteroid and abscisic acid in tomato responses to heat and oxidative stresses 
Journal of Experimental Botany  2014;65(15):4371-4383.
Summary
Brassinosteroids induce H2O2 accumulation from RBOH1-NADPH oxidase, which first induces ABA biosynthesis and stress tolerance, in turn leading to prolonged H2O2 production in both apoplast and chloroplast and stress tolerances.
The production of H2O2 is critical for brassinosteroid (BR)- and abscisic acid (ABA)-induced stress tolerance in plants. In this study, the relationship between BR and ABA in the induction of H2O2 production and their roles in response to heat and paraquat (PQ) oxidative stresses were studied in tomato. Both BR and ABA induced increases in RBOH1 gene expression, NADPH oxidase activity, apoplastic H2O2 accumulation, and heat and PQ stress tolerance in wild-type plants. BR could only induced transient increases in these responses in the ABA biosynthetic mutant notabilis (not), whereas ABA induced strong and prolonged increases in these responses in the BR biosynthetic mutant d ^im compared with wild-type plants. ABA levels were reduced in the BR biosynthetic mutant but could be elevated by exogenous BR. Silencing of RBOH1 compromised BR-induced apoplastic H2O2 production, ABA accumulation, and PQ stress responses; however, ABA-induced PQ stress responses were largely unchanged in the RBOH1-silenced plants. BR induces stress tolerance involving a positive feedback mechanism in which BR induces a rapid and transient H2O2 production by NADPH oxidase. The process in turn triggers increased ABA biosynthesis, leading to further increases in H2O2 production and prolonged stress tolerance. ABA induces H2O2 production in both the apoplastic and chloroplastic compartments.
doi:10.1093/jxb/eru217
PMCID: PMC4112640  PMID: 24899077
Abscisic acid; brassinosteroid; hydrogen peroxide; NADPH oxidase; Solanum lycopersicum; VIGS.
6.  RHBDL2 Is a Critical Membrane Protease for Anoikis Resistance in Human Malignant Epithelial Cells 
The Scientific World Journal  2014;2014:902987.
Anoikis resistance allows metastatic tumor cells to survive in a homeless environment. Activation of epithelial growth factor receptor (EGFR) signaling is one of the key mechanisms for metastatic tumor cells to resist anoikis, yet the regulation mechanisms of homeless-triggered EGFR activation in metastatic tumor cells remain unclear. Rhomboid-like-2 (RHBDL2), an evolutionally conserved intramembrane serine protease, can cleave the EGF ligand and thus trigger EGFR activation. Herein, we demonstrated that RHBDL2 overexpression in human epithelial cells resulted in promotion of cell proliferation, reduction of cell adhesion, and suppression of anoikis. During long-term suspension cultures, increased RHBDL2 was only detected in aggressive tumor cell lines. Treatment with the rhomboid protease inhibitor or RHBDL2 shRNA increased cleaved caspase 3, a marker of apoptosis. Finally, inhibition of EGFR activation increased the cleaved caspase 3 and attenuated the detachment-induced focal adhesion kinase phosphorylation. Taken together, these findings provide evidence for the first time that RHBDL2 is a critical molecule in anoikis resistance of malignant epithelial cells, possibly through the EGFR-mediated signaling. Our study demonstrates RHBDL2 as a new therapeutic target for cancer metastasis.
doi:10.1155/2014/902987
PMCID: PMC4058132  PMID: 24977233
7.  Chloroplastic thioredoxin-f and thioredoxin-m1/4 play important roles in brassinosteroids-induced changes in CO2 assimilation and cellular redox homeostasis in tomato 
Journal of Experimental Botany  2014;65(15):4335-4347.
Summary
Virus-induced gene silencing (VIGS) was used in this study to characterize the role of thioredoxin-f and thioredoxin-m1/4 in brassinosteroid-induced changes in CO2 assimilation and cellular redox homeostasis in tomato.
Chloroplast thioredoxins (TRXs) and glutathione function as redox messengers in the regulation of photosynthesis. In this work, the roles of chloroplast TRXs in brassinosteroids (BRs)-induced changes in cellular redox homeostasis and CO2 assimilation were studied in the leaves of tomato plants. BRs-deficient d ^im plants showed decreased transcripts of TRX-f, TRX-m2, TRX-m1/4, and TRX-x, while exogenous BRs significantly induced CO2 assimilation and the expression of TRX-f, TRX-m2, TRX-m1/4, and TRX-x. Virus-induced gene silencing (VIGS) of the chloroplast TRX-f, TRX-m2, TRX-m1/4, and TRX-y genes individually increased membrane lipid peroxidation and accumulation of 2-Cys peroxiredoxin dimers, and decreased the activities of the ascorbate–glutathione cycle enzymes and the ratio of reduced glutathione to oxidized glutathione (GSH/GSSG) in the leaves. Furthermore, partial silencing of TRX-f, TRX-m2, TRX-m1/4, and TRX-y resulted in decreased expression of genes involved in the Benson–Calvin cycle and decreased activity of the associated enzymes. Importantly, the BRs-induced increase in CO2 assimilation and the increased expression and activities of antioxidant- and photosynthesis-related genes and enzymes were compromised in the partially TRX-f- and TRX-m1/4-silenced plants. All of these results suggest that TRX-f and TRX-m1/4 are involved in the BRs-induced changes in CO2 assimilation and cellular redox homeostasis in tomato.
doi:10.1093/jxb/eru207
PMCID: PMC4112637  PMID: 24847092
Antioxidant; Benson–Calvin cycle; chloroplast; 2-Cys peroxiredoxin; glutathione; photosynthesis.
8.  Taxonomy of the genus Peyerimhoffia Kieffer from Mainland China, with a description of seven new species (Diptera, Sciaridae) 
ZooKeys  2014;67-83.
The taxonomy of the genus Peyerimhoffia Kieffer in China was studied. Eight species were recognized, including seven new species that are herein described and illustrated: P. hamata sp. n., P. obesa sp. n., P. sparsula sp. n., P. longiprojecta sp. n., P. brachypodua sp. n., P. yunnana sp. n., and P. shennongjiana sp. n. In addition, P. vagabunda (Winnertz, 1867) is reported for the first time from China. A key to these Chinese species is provided.
doi:10.3897/zookeys.382.4948
PMCID: PMC3950422  PMID: 24624020
Diptera; Sciaridae; new species; new record; China
9.  A functional variant in the cystathionine β-synthase gene promoter significantly reduces congenital heart disease susceptibility in a Han Chinese population 
Cell Research  2012;23(2):242-253.
Homocysteine is an independent risk factor for various cardiovascular diseases. There are two ways to remove homocysteine from embryonic cardiac cells: remethylation to form methionine or transsulfuration to form cysteine. Cystathionine β-synthase (CBS) catalyzes the first step of homocysteine transsulfuration as a rate-limiting enzyme. In this study, we identified a functional variant −4673C>G (rs2850144) in the CBS gene promoter region that significantly reduces the susceptibility to congenital heart disease (CHD) in a Han Chinese population consisting of 2 340 CHD patients and 2 270 controls. Individuals carrying the heterozygous CG and homozygous GG genotypes had a 15% (odds ratio (OR) = 0.85, 95% confidence interval (CI) = 0.75-0.96, P = 0.011) and 40% (OR = 0.60, 95% CI = 0.49-0.73, P = 1.78 × 10−7) reduced risk to develop CHD than the wild-type CC genotype carriers in the combined samples, respectively. Additional stratified analyses demonstrated that CBS −4673C>G is significantly related to septation defects and conotruncal defects. In vivo detection of CBS mRNA levels in human cardiac tissues and in vitro luciferase assays consistently showed that the minor G allele significantly increased CBS transcription. A functional analysis revealed that both the attenuated transcription suppressor SP1 binding affinity and the CBS promoter hypomethylation specifically linked with the minor G allele contributed to the remarkably upregulated CBS expression. Consequently, the carriers with genetically increased CBS expression would benefit from the protection due to the low homocysteine levels maintained by CBS in certain cells during the critical heart development stages. These results shed light on unexpected role of CBS and highlight the importance of homocysteine removal in cardiac development.
doi:10.1038/cr.2012.135
PMCID: PMC3567826  PMID: 22986502
congenital heart disease; cystathionine β-synthase; non-coding variant; homocysteine
10.  Exogenous abscisic acid application decreases cadmium accumulation in Arabidopsis plants, which is associated with the inhibition of IRT1-mediated cadmium uptake 
Cadmium (Cd) contamination of agricultural soils is an increasingly serious problem. Measures need to be developed to minimize Cd entering the human food chain from contaminated soils. We report here that, under Cd exposure condition, application with low doses of (0.1–0.5 μM) abscisic acid (ABA) clearly inhibited Cd uptake by roots and decreased Cd level in Arabidopsis wild-type plants (Col-0). Expression of IRT1 in roots was also strongly inhibited by ABA treatment. Decrease in Cd uptake and the inhibition of IRT1 expression were clearly lesser pronounced in an ABA-insensitive double mutant snrk2.2/2.3 than in the Col-0 in response to ABA application. The ABA-decreased Cd uptake was found to correlate with the ABA-inhibited IRT1 expression in the roots of Col-0 plants fed two different levels of iron. Furthermore, the Cd uptake of irt1 mutants was barely affected by ABA application. These results indicated that inhibition of IRT1 expression is involved in the decrease of Cd uptake in response to exogenous ABA application. Interestingly, ABA application increased the iron level in both Col-0 plants and irt1 mutants, suggesting that ABA-increased Fe acquisition does not depend on the IRT1 function, but on the contrary, the ABA-mediated inhibition of IRT1 expression may be due to the elevation of iron level in plants. From our results, we concluded that ABA application might increase iron acquisition, followed by the decrease in Cd uptake by inhibition of IRT1 activity. Thus, for crop production in Cd contaminated soils, developing techniques based on ABA application potentially is a promising approach for reducing Cd accumulation in edible organs in plants.
doi:10.3389/fpls.2014.00721
PMCID: PMC4267193  PMID: 25566293
abscisic acid; cadmium; cadmium translocation; iron; IRT1
11.  Identification of multiple salicylic acid-binding proteins using two high throughput screens 
Salicylic acid (SA) is an important hormone involved in many diverse plant processes, including floral induction, stomatal closure, seed germination, adventitious root initiation, and thermogenesis. It also plays critical functions during responses to abiotic and biotic stresses. The role(s) of SA in signaling disease resistance is by far the best studied process, although it is still only partially understood. To obtain insights into how SA carries out its varied functions, particularly in activating disease resistance, two new high throughput screens were developed to identify novel SA-binding proteins (SABPs). The first utilized crosslinking of the photo-reactive SA analog 4-AzidoSA (4AzSA) to proteins in an Arabidopsis leaf extract, followed by immuno-selection with anti-SA antibodies and then mass spectroscopy-based identification. The second utilized photo-affinity crosslinking of 4AzSA to proteins on a protein microarray (PMA) followed by detection with anti-SA antibodies. To determine whether the candidate SABPs (cSABPs) obtained from these screens were true SABPs, recombinantly-produced proteins were generated and tested for SA-inhibitable crosslinking to 4AzSA, which was monitored by immuno-blot analysis, SA-inhibitable binding of the SA derivative 3-aminoethylSA (3AESA), which was detected by a surface plasmon resonance (SPR) assay, or SA-inhibitable binding of [3H]SA, which was detected by size exclusion chromatography. Based on our criteria that true SABPs must exhibit SA-binding activity in at least two of these assays, nine new SABPs are identified here; nine others were previously reported. Approximately 80 cSABPs await further assessment. In addition, the conflicting reports on whether NPR1 is an SABP were addressed by showing that it bound SA in all three of the above assays.
doi:10.3389/fpls.2014.00777
PMCID: PMC4290489  PMID: 25628632
salicylic acid; salicylic acid-binding proteins; salicylic acid signaling; plant immunity; disease resistance
12.  RBOH1-dependent H2O2 production and subsequent activation of MPK1/2 play an important role in acclimation-induced cross-tolerance in tomato 
Journal of Experimental Botany  2013;65(2):595-607.
H2O2 and mitogen-activated protein kinase (MAPK) cascades play important functions in plant stress responses, but their roles in acclimation response remain unclear. This study examined the functions of H2O2 and MPK1/2 in acclimation-induced cross-tolerance in tomato plants. Mild cold, paraquat, and drought as acclimation stimuli enhanced tolerance to more severe subsequent chilling, photooxidative, and drought stresses. Acclimation-induced cross-tolerance was associated with increased transcript levels of RBOH1 and stress- and defence-related genes, elevated apoplastic H2O2 accumulation, increased activity of NADPH oxidase and antioxidant enzymes, reduced glutathione redox state, and activation of MPK1/2 in tomato. Virus-induced gene silencing of RBOH1, MPK1, and MPK2 or MPK1/2 all compromised acclimation-induced cross-tolerance and associated stress responses. Taken together, these results strongly suggest that acclimation-induced cross-tolerance is largely attributed to RBOH1-dependent H2O2 production at the apoplast, which may subsequently activate MPK1/2 to induce stress responses.
doi:10.1093/jxb/ert404
PMCID: PMC3904713  PMID: 24323505
Cross-tolerance; hydrogen peroxide; mitogen-activated protein kinase; reactive oxygen species; Respiratory burst oxidase homologue 1; signal transduction; Solanum lycopersicum.
13.  Stimulated Leaf Dark Respiration in Tomato in an Elevated Carbon Dioxide Atmosphere 
Scientific Reports  2013;3:3433.
It is widely accepted that leaf dark respiration is a determining factor for the growth and maintenance of plant tissues and the carbon cycle. However, the underlying effect and mechanism of elevated CO2 concentrations ([CO2]) on dark respiration remain unclear. In this study, tomato plants grown at elevated [CO2] showed consistently higher leaf dark respiratory rate, as compared with ambient control plants. The increased respiratory capacity was driven by a greater abundance of proteins, carbohydrates, and transcripts involved in pathways of glycolysis carbohydrate metabolism, the tricarboxylic acid cycle, and mitochondrial electron transport energy metabolism. This study provides substantial evidence in support of the concept that leaf dark respiration is increased by elevated [CO2] in tomato plants and suggests that the increased availability of carbohydrates and the increased energy status are involved in the increased rate of dark respiration in response to elevated [CO2].
doi:10.1038/srep03433
PMCID: PMC3852141  PMID: 24305603
14.  Comparison of male chimeric mice generated from microinjection of JM8.N4 embryonic stem cells into C57BL/6J and C57BL/6NTac blastocysts 
Transgenic research  2012;21(6):1149-1158.
To identify ways to improve the efficiency of generating chimeric mice via microinjection of blastocysts with ES cells, we compared production and performance of ES-cell derived chimeric mice using blastocysts from two closely related and commonly used sub-strains of C57BL/6. Chimeras were produced by injection of the same JM8.N4 (C57BL/6NTac) derived ES cell line into blastocysts of mixed sex from either C57BL/6J (B6J) or C57BL/6NTac (B6NTac) mice. Similar efficiency of production and sex-conversion of chimeric animals was observed with each strain of blastocyst. However, B6J chimeric males had fewer developmental abnormalities involving urogenital and reproductive tissues (1/12, 8%) compared with B6NTac chimeric males (7/9, 78%). The low sample size did not permit determination of statistical significance for many parameters. However, in each category analyzed the B6J-derived chimeric males performed as well, or better, than their B6NTac counterparts. Twelve of 14 (86%) B6J male chimeras were fertile compared with 6 of 11 (55%) B6NTac male chimeras. Ten of 12 (83%) B6J chimeric males sired more than 1 litter compared with only 3 of 6 (50%) B6NTac chimeras. B6J male chimeras produced more litters per productive mating (3.42 ± 1.73, n=12) compared to B6NTac chimeras (2.17 ± 1.33, n=6). Finally, a greater ratio of germline transmitting chimeric males was obtained using B6J blastocysts (9/14; 64%) compared with chimeras produced using B6NTac blastocysts (4/11; 36%). Use of B6J host blastocysts for microinjection of ES cells may offer improvements over blastocysts from B6NTac and possibly other sub-strains of C57BL/6 mice.
doi:10.1007/s11248-012-9605-3
PMCID: PMC3445772  PMID: 22422470
ES cell chimeric mice; C57BL/6J; JM8.N4 ES cells
15.  High-performance solid-state supercapacitors based on graphene-ZnO hybrid nanocomposites 
Nanoscale Research Letters  2013;8(1):473.
In this paper, we report a facile low-cost synthesis of the graphene-ZnO hybrid nanocomposites for solid-state supercapacitors. Structural analysis revealed a homogeneous distribution of ZnO nanorods that are inserted in graphene nanosheets, forming a sandwiched architecture. The material exhibited a high specific capacitance of 156 F g−1 at a scan rate of 5 mV.s−1. The fabricated solid-state supercapacitor device using these graphene-ZnO hybrid nanocomposites exhibits good supercapacitive performance and long-term cycle stability. The improved supercapacitance property of these materials could be ascribed to the increased conductivity of ZnO and better utilization of graphene. These results demonstrate the potential of the graphene-ZnO hybrid nanocomposites as an electrode in high-performance supercapacitors.
doi:10.1186/1556-276X-8-473
PMCID: PMC3842674  PMID: 24215772
Zinc oxide nanorods; Graphene nanosheets; Solid-state supercapacitor
16.  Severe Multiple Necrotizing Fasciitis Complicated by Abdominal Compartment Syndrome in an Infant 
Iranian Journal of Pediatrics  2013;23(5):601-603.
PMCID: PMC4006514  PMID: 24800025
Necrotizing Fasciitis; Abdominal Compartment Syndrome; Negative-Pressure Wound Therapy; Infant
17.  The Role of Hydrogen Peroxide and Nitric Oxide in the Induction of Plant-Encoded RNA-Dependent RNA Polymerase 1 in the Basal Defense against Tobacco Mosaic Virus 
PLoS ONE  2013;8(9):e76090.
Plant RNA-dependent RNA Polymerase 1 (RDR1) is an important element of the RNA silencing pathway in the plant defense against viruses. RDR1 expression can be elicited by viral infection and salicylic acid (SA), but the mechanisms of signaling during this process remains undefined. The involvement of hydrogen peroxide (H2O2) and nitric oxide (NO) in RDR1 induction in the compatible interactions between Tobacco mosaic tobamovirus (TMV) and Nicotiana tabacum, Nicotiana benthamiana, and Arabidopsis thaliana was examined. TMV inoculation onto the lower leaves of N. tabacum induced the rapid accumulation of H2O2 and NO followed by the increased accumulation of RDR1 transcripts in the non-inoculated upper leaves. Pretreatment with exogenous H2O2 and NO on upper leaf led to increased RDR1 expression and systemic TMV resistance. Conversely, dimethylthiourea (an H2O2 scavenger) and 2-(4-carboxyphenyl)- 4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (an NO scavenger) partly blocked TMV- and SA-induced RDR1 expression and increased TMV susceptibility, whereas pretreatment with exogenous H2O2 and NO failed to diminish TMV infection in N. benthamiana plants with naturally occurring RDR1 loss-of-function. Furthermore, in N. tabacum and A. thaliana, TMV-induced H2O2 accumulation was NO-dependent, whereas NO generation was not affected by H2O2. These results suggest that, in response to TMV infection, H2O2 acts downstream of NO to mediate induction of RDR1, which plays a critical role in strengthening RNA silencing to restrict systemic viral infection.
doi:10.1371/journal.pone.0076090
PMCID: PMC3786905  PMID: 24098767
18.  Cytokinin-Induced Parthenocarpic Fruit Development in Tomato Is Partly Dependent on Enhanced Gibberellin and Auxin Biosynthesis 
PLoS ONE  2013;8(7):e70080.
Fruit set of plants largely depends on the biosynthesis and crosstalk of phytohormones. To date the role of cytokinins (CKs) in the fruit development is less understood. Here, we showed that parthenocarpic fruit could be induced by 1-(2-chloro-4-pyridyl)-3-phenylurea (CPPU, an active CK) in tomato (Solanumlycopersicum cv. Micro-Tom). The fresh weight of CPPU-induced parthenocarpic fruits was comparable with that induced by GA3. Importantly, CPPU-induced parthenocarpy was found to be compromised by simultaneous application of paclobutrazol (a GA biosynthesis inhibitor), and this effect could be restored by exogenous GA3. Like pollination, CPPU-induced fruit showed enhanced accumulation of GA1+3 and indole-3-acetic (IAA), which were accompanied by elevated expression of GA biosynthesis genes like SlGPS, SlGA20ox1, SlGA20ox2 and SlGA3ox1, and IAA biosynthesis gene ToFZY. Elevated GAs level in CPPU-induced fruits was also associated with down-regulation of GA inactivation genes, namely SlGA2ox1,2,3,4,5 in comparison with untreated control. These results suggested that CKs may induce parthenocarpy in tomato partially through modulation of GA and IAA metabolisms.
doi:10.1371/journal.pone.0070080
PMCID: PMC3726760  PMID: 23922914
19.  Detection of Deregulated Modules Using Deregulatory Linked Path 
PLoS ONE  2013;8(7):e70412.
The identification of deregulated modules (such as induced by oncogenes) is a crucial step for exploring the pathogenic process of complex diseases. Most of the existing methods focus on deregulation of genes rather than the links of the path among them. In this study, we emphasize on the detection of deregulated links, and develop a novel and effective regulatory path-based approach in finding deregulated modules. Observing that a regulatory pathway between two genes might involve in multiple rather than a single path, we identify condition-specific core regulatory path (CCRP) to detect the significant deregulation of regulatory links. Using time-series gene expression, we define the regulatory strength within each gene pair based on statistical dependence analysis. The CCRPs in regulatory networks can then be identified using the shortest path algorithm. Finally, we derive the deregulated modules by integrating the differential edges (as deregulated links) of the CCRPs between the case and the control group. To demonstrate the effectiveness of our approach, we apply the method to expression data associated with different states of Human Epidermal Growth Factor Receptor 2 (HER2). The experimental results show that the genes as well as the links in the deregulated modules are significantly enriched in multiple KEGG pathways and GO biological processes, most of which can be validated to suffer from impact of this oncogene based on previous studies. Additionally, we find the regulatory mechanism associated with the crucial gene SNAI1 significantly deregulated resulting from the activation of HER2. Hence, our method provides not only a strategy for detecting the deregulated links in regulatory networks, but also a way to identify concerning deregulated modules, thus contributing to the target selection of edgetic drugs.
doi:10.1371/journal.pone.0070412
PMCID: PMC3722188  PMID: 23894653
20.  Brassinosteroids-Induced Systemic Stress Tolerance was Associated with Increased Transcripts of Several Defence-Related Genes in the Phloem in Cucumis sativus 
PLoS ONE  2013;8(6):e66582.
Brassinosteroids (BRs), a group of naturally occurring plant steroidal compounds, are essential for plant growth, development and stress tolerance. Recent studies showed that BRs could induce systemic tolerance to biotic and abiotic stresses; however, the molecular mechanisms by which BRs signals lead to responses in the whole plant are largely unknown. In this study, 24-epibrassinosteroid (EBR)-induced systemic tolerance in Cucumis sativus L. cv. Jinyan No. 4 was analyzed through the assessment of symptoms of photooxidative stress by chlorophyll fluorescence imaging pulse amplitude modulation. Expression of defense/stress related genes were induced in both treated local leaves and untreated systemic leaves by local EBR application. With the suppressive subtractive hybridization (SSH) library using cDNA from the phloem sap of EBR-treated plants as the tester and distilled water (DW)-treated plants as the driver, 14 transcripts out of 260 clones were identified. Quantitative Real Time-Polymerase Chain Reaction (RT-qPCR) validated the specific up-regulation of these transcripts. Of the differentially expressed transcripts with known functions, transcripts for the selected four cDNAs, which encode an auxin-responsive protein (IAA14), a putative ankyrin-repeat protein, an F-box protein (PP2), and a major latex, pathogenesis-related (MLP)-like protein, were induced in local leaves, systemic leaves and roots after foliar application of EBR onto mature leaves. Our results demonstrated that EBR-induced systemic tolerance is accompanied with increased transcript of genes in the defense response in other organs. The potential role of phloem mRNAs as signaling components in mediating BR-regulated systemic resistance is discussed.
doi:10.1371/journal.pone.0066582
PMCID: PMC3686678  PMID: 23840504
21.  Proteomic analysis of energy metabolism and signal transduction in irradiated melanoma cells 
AIM
To analyze proteomic and signal transduction alterations in irradiated melanoma cells.
METHODS
We combined stable isotope labeling with amino acids in cell culture (SILAC) with highly sensitive shotgun tandem mass spectrometry (MS) to create an efficient approach for protein quantification. Protein-protein interaction was used to analyze relationships among proteins.
RESULTS
Energy metabolism protein levels were significantly different in glycolysis and not significantly different in oxidative phosphorylation after irradiation. Conversely, tumor suppressor proteins related to cell growth and development were downregulated, and those related to cell death and cell cycle were upregulated in irradiated cells.
CONCLUSION
Our results indicate that irradiation induces differential expression of the 29 identified proteins closely related to cell survival, cell cycle arrest, and growth inhibition. The data may provide new insights into the pathogenesis of uveal melanoma and guide appropriate radiotherapy.
doi:10.3980/j.issn.2222-3959.2013.03.06
PMCID: PMC3693007  PMID: 23826520
melanoma cell; 2D-LC-MS/MS; stable isotope labeling with amino acids; proteomic analysis; X-ray irradiation; protein-protein interaction
22.  Evaluation of treatment response for breast cancer: are we entering the era of “biological complete remission”? 
Breast cancer is one of the most common malignancies in women. The post-operative recurrence and metastasis are the leading causes of breast cancer-related mortality. In this study, we tried to explore the role of circulating tumor cell (CTC) detection combination PET/CT technology evaluating the prognosis and treatment response of patients with breast cancer; meanwhile, we attempted to assess the concept of “biological complete remission” (bCR) in this regard. A 56-year-old patient with breast cancer (T2N1M1, stage IV left breast cancer, with metastasis to axillary lymph nodes and lungs) received 6 cycles of salvage treatment with albumin-bound paclitaxel plus capecitabine and trastuzumab. Then, she underwent CTC detection and PET/CT for efficacy evaluation. CTC detection combination PET/CT is useful for the evaluation of the biological efficacy of therapies for breast cancer. The bCR of the patient appeared earlier than the conventional clinical imaging complete remission and promised the histological (pathological) complete remission. The integrated application of the concepts including bCR, imageological CR, and histological CR can achieve the early and accurate assessment of biological therapeutic reponse and prognosis of breast cancer.
doi:10.3978/j.issn.1000-9604.2012.11.01
PMCID: PMC3551336  PMID: 23359646
Breast cancer; circulating tumor cell; PET/CT; biological complete remission
23.  Role of brassinosteroids in alleviation of phenanthrene–cadmium co-contamination-induced photosynthetic inhibition and oxidative stress in tomato 
Journal of Experimental Botany  2012;64(1):199-213.
Heavy metal pollution often occurs together with organic contaminants. Brassinosteroids (BRs) induce plant tolerance to several abiotic stresses, including phenanthrene (PHE) and cadmium (Cd) stress. However, the role of BRs in PHE+Cd co-contamination-induced stress amelioration is unknown. Here, the interactive effects of PHE, Cd, and 24-epibrassinolide (EBR; a biologically active BR) were investigated in tomato plants. The application of Cd (100 µM) alone was more phytotoxic than PHE applied alone (100 µM); however, their combined application resulted in slightly improved photosynthetic activity and pigment content compared with Cd alone after a 40 d exposure. Accumulation of reactive oxygen species and membrane lipid peroxidation were induced by PHE and/or Cd; however, the differences in effect were insignificant between Cd and PHE+Cd. The foliar application of EBR (0.1 µM) to PHE- and/or Cd-stressed plants alleviated photosynthetic inhibition and oxidative stress by causing enhancement of the activity of the enzymes and related transcript levels of the antioxidant system, secondary metabolism, and the xenobiotic detoxification system. Additionally, PHE and/or Cd residues were significantly decreased in both the leaves and roots after application of EBR, more specifically in PHE+Cd-stressed plants when treated with EBR, indicating a possible improvement in detoxification of these pollutants. The findings thus suggest a potential interaction of EBR and PHE for Cd stress alleviation. These results advocate a positive role for EBR in reducing pollutant residues for food safety and also strengthening phytoremediation.
doi:10.1093/jxb/ers323
PMCID: PMC3528031  PMID: 23201830
Brassinosteroids; food safety; heavy metal; photosynthesis; phytoremediation; polycyclic aromatic hydrocarbons (PAHs)
24.  Valence band offset of β-Ga2O3/wurtzite GaN heterostructure measured by X-ray photoelectron spectroscopy 
Nanoscale Research Letters  2012;7(1):562.
A sample of the β-Ga2O3/wurtzite GaN heterostructure has been grown by dry thermal oxidation of GaN on a sapphire substrate. X-ray diffraction measurements show that the β-Ga2O3 layer was formed epitaxially on GaN. The valence band offset of the β-Ga2O3/wurtzite GaN heterostructure is measured by X-ray photoelectron spectroscopy. It is demonstrated that the valence band of the β-Ga2O3/GaN structure is 1.40 ± 0.08 eV.
doi:10.1186/1556-276X-7-562
PMCID: PMC3526396  PMID: 23046910
β-Ga2O3/wurtzite GaN heterostructure; Band offset; X-ray photoelectron spectroscopy
25.  Hydrogen peroxide functions as a secondary messenger for brassinosteroids-induced CO2 assimilation and carbohydrate metabolism in Cucumis sativus *  
Brassinosteroids (BRs) are potent regulators of photosynthesis and crop yield in agricultural crops; however, the mechanism by which BRs increase photosynthesis is not fully understood. Here, we show that foliar application of 24-epibrassinolide (EBR) resulted in increases in CO2 assimilation, hydrogen peroxide (H2O2) accumulation, and leaf area in cucumber. H2O2 treatment induced increases in CO2 assimilation whilst inhibition of the H2O2 accumulation by its generation inhibitor or scavenger completely abolished EBR-induced CO2 assimilation. Increases of light harvesting due to larger leaf areas in EBR- and H2O2-treated plants were accompanied by increases in the photochemical efficiency of photosystem II (ΦPSII) and photochemical quenching coefficient (q P). EBR and H2O2 both activated carboxylation efficiency of ribulose-1,5-bisphosphate oxygenase/carboxylase (Rubisco) from analysis of CO2 response curve and in vitro measurement of Rubisco activities. Moreover, EBR and H2O2 increased contents of total soluble sugar, sucrose, hexose, and starch, followed by enhanced activities of sugar metabolism such as sucrose phosphate synthase, sucrose synthase, and invertase. Interestingly, expression of transcripts of enzymes involved in starch and sugar utilization were inhibited by EBR and H2O2. However, the effects of EBR on carbohydrate metabolisms were reversed by the H2O2 generation inhibitor diphenyleneodonium (DPI) or scavenger dimethylthiourea (DMTU) pretreatment. All of these results indicate that H2O2 functions as a secondary messenger for EBR-induced CO2 assimilation and carbohydrate metabolism in cucumber plants. Our study confirms that H2O2 mediates the regulation of photosynthesis by BRs and suggests that EBR and H2O2 regulate Calvin cycle and sugar metabolism via redox signaling and thus increase the photosynthetic potential and yield of crops.
doi:10.1631/jzus.B1200130
PMCID: PMC3468824  PMID: 23024048
Metabolism; Photosynthesis; Reactive oxygen species; Rubisco; Sucrose

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