Proteome analysis of the plant-pathogenic bacterium Xanthomonas oryzae pv. oryzae

The plant-pathogenic bacterium Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of bacterial blight, which is one of the most serious diseases of rice. Xoo has been studied for over one century, and much has been learned about it, but proteomic investigation has been neglected. In this study, proteome reference maps of Xoo were constructed by two-dimensional gel electrophoresis, and 628 spots in the gels representing 469 different protein species were identified with MALDI-TOF/TOF MS. The identified spots were assigned to 15 functional categories according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and the annotations from the National Center for Biotechnology Information (NCBI) database. The data set has been deposited in the World-2DPAGE database (Database ID: 0044). In addition, comparative proteomic analysis revealed that proteins related to the TonB-dependent transportation system and energy metabolism are involved in the phenazine-1-carboxylic acid resistance in Xoo. In conclusion, we have established a proteome database for Xoo and have used this database in a comparative proteomic analysis that identified proteins potentially contributing to phenazine-1-carboxylic acid resistance in Xoo.     

The biological control of Pomacea canaliculata population by rice-duck mutualism in paddy fields

Duck has been used as a non-chemical control method against Pomacea canaliculata Lamarck, but little is known about its principles that underlie the control of snail populations. An indoor experiment was initially used to observe the predation potential of ducks, followed by replicated field trials. In the indoor studies, ducks effectively preyed on juvenile snails, but had a weak predatory effect on large snails and egg clusters. In the field, application of a rice-duck mutualism system significantly reduced the numbers of snails (especially number of immature individuals), number of snail egg clusters and snail damage to rice plants. The controlling effect was longer and more stable than the chemical application, resulting in a better yield than with the pentachlorophenol sodium and tea seed powder treatment. Our experimental results also suggested that the snail age structure in the rice-duck mutualism plots was shifted towards older snails by ducks preying, indicating a trend towards population decline, and ducks caused snails to oviposit on sites not ideal for hatchling establishment. Throughout the studies, it is suggested that a rice-duck mutualism system could be used for controlling P. canaliculata in organic rice production.     

Systematic study of human long intergenic non-coding RNAs and their impact on cancer

The functional impact of several long intergenic non-coding RNAs (lincRNAs) has been characterized in previous studies. However, it is difficult to identify lincRNAs on a large-scale and to ascertain their functions or predict their structures in laboratory experiments because of the diversity, lack of knowledge and specificity of expression of lincRNAs. Furthermore, although there are a few well-characterized examples of lincRNAs associated with cancers, these are just the tip of the iceberg owing to the complexity of cancer. Here, by combining RNA-Seq data from several kinds of human cell lines with chromatin-state maps and human expressed sequence tags, we successfully identified more than 3000 human lincRNAs, most of which were new ones. Subsequently, we predicted the functions of 105 lincRNAs based on a coding-non-coding gene co-expression network. Finally, we propose a genetic mediator and key regulator model to unveil the subtle relationships between lincRNAs and lung cancer. Twelve lincRNAs may be principal players in lung tumorigenesis. The present study combines large-scale identification and functional prediction of human lincRNAs, and is a pioneering work in characterizing cancer-associated lincRNAs by bioinformatics.     

At-line near-infrared spectroscopy for monitoring concentrations in temperature-triggered glutamate fermentation

Rapid development in the glutamate fermentation industry has dictated the need for effective fermentation monitoring by rapid and precise methods that provide real-time information for quality control of the end-product. In recent years, near-infrared (NIR) spectroscopy and multivariate calibration have been developed as fast, inexpensive, non-destructive and environmentally safe techniques for industrial applications. The purpose of this study was to develop models for monitoring glutamate, glucose, lactate and alanine concentrations in the temperature-triggered process of glutamate fermentation. NIR measurements of eight batches of samples were analyzed by partial least-squares regression with several spectral pre-processing methods. The coefficient of determination (R ²), model root-mean square error of calibration (RMSEC), root-mean square error of prediction (RMSEP) and residual predictive deviation (RPD) of the test calibration for the glutamate concentration were 0.997, 3.11 g/L, 2.56 g/L and 19.81, respectively. For the glucose concentration, R ², RMSEC, RMSEP and RPD were 0.989, 1.37 g/L, 1.29 g/L and 9.72, respectively. For the lactate concentration, R ², RMSEC, RMSEP and RPD were 0.975, 0.078 g/L, 0.062 g/L and 6.29, respectively. For the alanine concentration, R ², RMSEC, RMSEP and RPD were 0.964, 0.213 g/L, 0.243 g/L and 5.29, respectively. New batch fermentation as an external validation was used to check the models, and the results suggested that the predictive capacity of the models for the glutamate fermentation process was good.     

Functional Nucleic Acid Nanoparticle-Based Resonance Scattering Spectral Probe

Highly sensitive and selective resonance Rayleigh scattering (RRS) and surface enhanced resonance Raman scattering (SERRS) spectral detection technique are developed by combining the functional nucleic acid including aptamer and DNAzyme, and nanoparticle such as gold/silver (NG/NS) aggregation and catalysis reaction. The recent progress of resonance scattering spectral technologies including RRS and SERRS are reviewed in this paper.     

Comparison between drug-induced and K+-induced changes in molar acid extrusion fluxes (JH +) and in energy consumption rates in astrocytes

Neuronal excitation leads to an increase of the extracellular K⁺ concentration ([K⁺]_o) in brain. This increase has at least two energy-consuming consequences: (1) a depolarization-mediated change in intracellular pH (pH_i) in astrocytes due to depolarization-mediated increased activity of the acid-extruding Na⁺/bicarbonate transporter NBCe1 (driven by secondary active transport, supported by ion gradients established by the Na⁺, K⁺-ATPase); and (2) activation of cellular reuptake of K⁺ mediated by the Na⁺, K⁺-ATPase in both neurons and astrocytes. Astrocytic, but not neuronal increase in NBCe1 activity and pH_i is also seen after chronic treatment with either of the two anti-bipolar drugs carbamazepine or valproic acid. The third ‘classical’ anti-bipolar drug, ‘lithium’ increases astrocytic pH_i by a different mechanism (stimulation of the acid extruding Na⁺/H⁺ exchanger NHE1). The acid extruder fluxes, which depend upon the change in pH_i per time unit (ΔpH_i/Δt) and intracellular buffering power, have not been established in most of these situations. Therefore their stimulatory effects on energy metabolism has not been quantitated. This has been done in the present study in cultured mouse astrocytes. pH_i was determined using the fluorescent pH-sensitive indicator BCECF–AM and an Olympus IX71 live cell imaging fluorescence microscope. Molar acid extrusion fluxes (indicating transporter activity) were determined as pH_i changes/min during recovery after acid-loading with NH₃/NH₄ ⁺, NBCe1 mRNA and protein expression in the cultured cells by, respectively RT-PCR and Western blotting. Drug-induced up-regulation of acid extrusion flux was slow and less than physiologically seen after increase in K⁺ concentration. Energetically, K⁺ uptake is much costlier than NBCe1 activity.     

Quantification of 8-iso-prostaglandin-F(2alpha) and 2,3-dinor-8-iso-prostaglandin-F(2alpha) in human urine using liquid chromatography-tandem mass spectrometry

Quantification of 8-iso-prostaglandin F(2alpha) (8-iso-PGF(2alpha)) has been suggested to be a reliable indicator of lipid peroxidation that may be related to in vivo free radical generation, oxidative damage, and antioxidant deficiency. We have developed a LC-MS/MS method to quantify 8-iso- PGF(2alpha) and its dinor metabolite, 2,3-dinor-8-iso-prostaglandin F(2alpha) (2,3-dinor-8-iso-PGF(2alpha)), in human urine samples. After an initial purification step using an automated C18 solid phase extraction procedure, the urine sample was injected directly into a liquid chromatography (LC) system and detected with tandem mass spectrometry. The detection limit of the assay was 9 pg for 8-iso-PGF(2alpha) and 3 pg for 2,3-dinor-8-iso-PGF(2alpha) with both inter- and intraday variations of less than 12%. The inaccuracies were less than 3% for both analytes at three different levels. The urinary excretion rate of 2,3-dinor-8-iso-PGF(2alpha) was higher than that of 8-iso-PGF(2alpha), and changed in proportion to the parent compound (R = 0.70, n = 60). Values obtained with this method showed good linear correlation to duplicate 8-iso-PGF(2alpha) measurements performed with GCMS (R = 0.97, n = 15). The mean excretion rates of 8-iso-PGF(2alpha) and 2,3-dinor-8-iso-PGF(2alpha) were significantly higher in smokers than in nonsmokers (0.53 +/- 0.37 vs. 0.25 +/- 0.15 microg/g creatinine, p = 0.002 for 8-iso-PGF(2alpha) and 8.9 +/- 3.8 vs. 4.6 +/- 2.6 microg/g creatinine, p = 0.003 for 2,3-dinor-8-iso-PGF(2alpha), respectively). The excellent accuracy, reproducibility, and high throughput of this method should permit it to be used in large clinical studies and standard clinical laboratories.     

环境激素DBP对拟南芥试管形态发生的影响

报道了酞酸酯类化合物DBP对拟南芥试管形态发生的影响。利用不同浓度的DBF处理拟南芥茎段外植体,切片观察拟南芥茎段试管形态发生过程中脱分化、分化及再分化的变化情况。结果发现：拟南芥茎段外植体在对照组培养基上生长良好,首先是愈伤组织产生,而后愈伤组织块增大,颜色呈淡绿色,生长旺盛,并有分化出芽现象;添加0．01mg／L、0．1mg／L和1．0mg／LDBP,茎段愈伤组织诱导率低,且高浓度时愈伤组织出现褐化、活力差的现象;培养12h、24h、2d、3d、7d、14d、21d和28d茎段显微切片结果显示,DBP具有抑制拟南芥试管形态发生的作用,随着DBP浓度的增加呈现剂量抑制效应。