小麦赤霉病穗组织中亚洲镰刀菌定量分析及其在品种(系)抗性评价中的应用

为探明小麦穗中亚洲镰刀菌Fusarium asiaticum积累菌量与品种赤霉病抗性的关系,并探讨该菌定量分析方法在品种抗性评价中的应用价值,用TaqMan探针实时荧光定量PCR法对接种5d和10d后的9个小麦品种(系)穗组织中的F.asiaticum DNA进行测定,并与相应品种(系)田间抗性调查结果进行比较。结果表明,在F.asiaticum DNA定量检测中,Taq Man探针实时PCR技术具有高度的稳定性和可重复性。小麦品种间F.asiaticumDNA含量差异显著,接种10d后比接种5d后的DNA检测结果更能真实地反映不同品种(系)之间抗性水平的差异。在田间表现中抗水平的品种(系)之间接种10d后F.asiaticumDNA含量也有显著差异。与田间鉴定结果比较,定量分析具有较好的区分作用。

More attention should be paid on the interpretation of gene expression data

Molecular profiling of gene expression is important for determining signatures in cancer progression and diagnosis.For this purpose,polymerase chain reactionbased techniques are preferentially used as a feasible and sensitive approach.Nevertheless,when relative quantitative analyses are performed on gene expression,the interpretation of mathematical equations must be carefully done.This letter to the editor is focused on recently published gene expression data in World Journal of Gastroenterology by Ozmen et al demonstrating increased levels of LYVE-1,VEGFR-3 and CD44 genes in gastric cancer samples compared to nonneoplastic gastric tissues.However,there are major concerns about misinterpretation of the gene expression data obtained with the 2-ΔΔCt relative quantitative method.In the study,2-ΔΔCt values calculated for many samples were smaller than 1(2-ΔΔCt < 1) which indicate decreased levels of LYVE-1,VEGFR-3 and CD44 gene expression in the gastric cancer tissues.This unfortunate mistake is an important example showing how a simple error in the interpretation of relative-quantitative gene expression data may result in misleading scientific conclusions.In this letter,a brief explanation of the 2-ΔΔCt method is given.In addition,the importance of technical quality and interpretation in gene expression studies is discussed.

Rice Repetitive DNA Sequence RRD3:a Plant Promoter and Its Application to RNA Interference

Previously, a moderately repetitive DNA sequence （RRD3） was cloned from rice （Oryza sativa L.） by DNA renaturation kinetics. Sequence analysis revealed several conserved promoter motifs, including four TATA-boxes and a CAAT-box, and promoter activity was shown in Escherichia coli and mammalian expression systems. Here, we inserted the RRD3 fragment into the plant promoter-capture vector, pCAMBIA1391Z, and examined whether the RRD3 fragment has promoter activity in plants. Transgenic tobacco and rice calli both showed β-glucuronidase （GUS） activity, indicating that RRD3 can act as a promoter in both monocot and dicot plants. Based on the promoter characteristic of RRD3, we designed a plant universal binary vector, pCRiRRD3, which is suitable for performing researches on plant RNA interference. This vector has two multiple cloning sites to facilitate sense and antisense cloning of the target sequence, separated by an intron fragment of 200 bp. The efficiency of the vector for gene silencing was assayed by histochemical and quantitative fluorometric GUS assays in transgenic tobacco. These research results suggested that this plant RNAi vector pCRiRRD3 can effectively perform gene silencing researches on both monocot and dicot plants.

Molecular Modeling and Design of Arylthioindole Derivatives as Tubulin Inhibitors

Three-dimensional quantitative structure activity relationship （3D-QSAR） and docking studies of a series of arylthioindole derivatives as tubulin inhibitors against human breast cancer cell line MCF-7 have been carried out. An optimal 3D-QSAR model from the comparative molecular field analysis （CoMFA） for training set with significant statistical quality （R2=0.898） and predictive ability （q2=0.654） was established. The same model was further applied to predict pIC50 values of the compounds in test set, and the resulting predictive correlation coefficient R2（pred） reaches 0.816, further showing that this CoMFA model has high predictive ability. Moreover, the appropriate binding orientations and conformations of these compounds interacting with tubulin are located by docking study, and it is very interesting to find the consistency between the CoMFA field distribution and the 3D topology structure of active site of tubulin. Based on CoMFA along with docking results, some important factors improving the activities of these compounds were discussed in detail and were summarized as follows： the substituents R3-R5 （on the phenyl ring） with higher electronegativity, the substituent R6 with higher eleetropositivity and bigger bulk, the substituent R7 with smaller bulk, and so on. In addition, five new compounds with higher activities have been designed. Such results can offer useful theoretical references for experimental works.

3D-QSAR and action mechanism of potential dual inhibitors towards AP-1 and NF-κB

Three-dimensional quantitative structure-activity relationship （3D-QSAR） and docking studies of a series of novel dioxopyrrolinyl-amino-pyrimidine derivatives, which are potential dual inhibitors mediating a transcriptional activation towards protein-1 （AP-1） and nuclear factor kappa B （NF-κB）, have been carried out. The QS, AR models established by comparative molecular field analysis （CoMFA） and comparative molecular similarity index analysis （CoMSIA） show a good predictive ability with cross-validated coefficients q2 of 0.644 and 0.636, respectively. The docking result shows that there are quite lower average values of the flexible and rigid energy scores on the selected binding sites, meanwhile, it further shows that the binding sites just fall on the joint regions between AP-1 （and NF-κB） and DNA. The reason that these analogues have inhibition function towards AP-I and NF-κB is that their existence on these joint regions can effectively prevent free AP-I and NF-κB from binding to DNA. These results can offer a valuable theoretical reference to the pharmaceutical molecular design as well as the action mechanism analysis.

Theoretical Study on Xe…N non-Covalent Interactions:Three Hybridization N with XeO_(3) and XeOF_(2)

The interactions of complexes of XeOF_(2) and XeO_(3) with a series of different hybridization N-containing donors are studied by means of DFT and MP_(2) calculations.The aerogen bonding interaction energies range from 6.5 kcal/mol to19.9 kcal/mol between XeO_(3) or XeOF_(2) and typical N-containing donors.The sequence of interaction for N-containing hy-bridization is sp^(3)>sp^(2)>sp,and XeO_(3)is higher than XeOF_(2).For some donors of sp^(2)and sp^(3) hybridization,the steric effect plays a minor role in the interaction with the evidence of reduced density gradient plots.The dominant stable part is the electrostatic interaction.In complex of XeO_(3),the weight of polarization is larger than dispersion,while the situation is opposite for XeOF_(2)complexes.Except for the sum of the maximum value of molecular electrostatic potential on Xe atom and minimum value of molecular electrostatic potential on N atom,the other five interaction parameters including the potential energy density at bond critical point,the equilibrium distances,interaction energies with the basis set superposition error correction,localized molecular orbital energy decomposition analysis interaction energies,and the electron charge density,show great linear correlation coefficients with each other.

Studying the current properties of buffer solution through micro-fluidic channels driven with the pulse bias

In the research of bio-molecular chips and sensors, extra electric biases are most often employed to control and manipulate the DNA and protein molecules moving through micro/nano-fluidic channels. In order to accurately and flexibly control the bio-molecules as they move within the channels, a clear understanding of how the current changes within the buffer solution caused by an applied bias is fundamental. In this report, the current changed value of different buffer solutions, e.g., KC1, TE, and TBE was systematically studied with real-time monitoring and quantitative analysis in the situation of the buffers moving through a fluidic channel with a 5 μm inner diameter, driven by biases of 50 or 100 mV. The results revealed that the relation- ship between the current changed value and the pause interval of the applied electric field is highly consistent with the Hill Equation, which is helpful for accurately detecting and manipulating single biomolecules in microfluidic sensors and biochips.

3D-QSAR and docking studies on 2-arylbenzoxazole and linker-Y transthyretin amyloidogenesis inhibitors

Transthyretin(TTR),a plasma protein with a tetramer structure,could form amyloid fibril associated with several human diseases through the dissociation of tetramer and the misfolding of monomer.These amyloidogenesis can be inhibited by small molecules which bind to the central channel of TTR.A number of small molecules like 2-arylbenzoxazoles(ABZ)analogues are proposed as promising therapeutic strategy to treat amyloidosis.In this work,comparative molecular field analysis(CoMFA)and comparative molecular similarity indices analysis(CoMSIA)three-dimensional quantitative structure-activity relationship(3D-QSAR)and docking studies were performed on series of 2-arylbenzoxazoles(ABZ)and linker-Y analogues to investigate the inhibitory activities of TTR amyloidogenesis at atomic level.Significant correlation coefficients for ABZ series(CoMFA,r2=0.877,q2=0.431;CoMSIA,r2=0.836,q2=0.447)and those for linker-Y series(CoMFA,r2=0.828,q2=0.522;CoMSIA,r2=0.800,q2=0.493)were obtained,and the generated models were validated using test sets.In addition,docking studies on 6 compounds binding to TTR were performed to analyze the forward or reverse binding mode and interactions between molecules and TTR.These results from 3D-QSAR and docking studies have great significance for designing novel TTR amyloidogenesis inhibitors in the future.