利用功能基因组学方法研究SMAD去磷酸化-TGF-β超家族信号转导的终止机制

在后生动物机体中,转化生长因子β(TGF-β)及相关生长因子可以通过自分泌、旁分泌及内分泌方式影响广泛的生理活动。它们在多种疾病的发病过程中起着重要的作用,尤其是癌症、纤维化疾病、自免疫疾病和心血管系统疾病。TGF-β受体介导的R-SMADs的磷酸化是TGF-β信号转导通路中最重要的步骤,引起从细胞质内SMAD复合体的组装到核内转录调控这样一个细胞内的信号转导。因此,R-SMADs的去磷酸化是TGF-β信号转导终止的一个重要的机制。最近,我们实验室结合功能基因组学、生物化学和发育生物学的方法,鉴定并研究了磷酸酶PPM1在TGF-β信号转导调控中的功能。文章简短地总结了SMADs动态的磷酸化和去磷酸化是如何调控信号转导的强度和持久性以及TGF-β信号转导的生理功能。     

The determination of potassium concentration in vitreous humor by low pressure ion chromatography and its application in the estimation of postmortem interval

An analytical method was developed for the determination of potassium in vitreous humor by low pressure ion chromatography (LPIC). Experimental conditions for LPIC analysis were optimized. High sensitivity and selectivity were obtained using this method. The LOD and LOQ were 1 and 2 mmol l(-1), respectively. The linearity was demonstrated from 2 to 20 mmol l(-1). The intra- and inter-day precision (CV) based on three concentrations was less than 5.0%. It was a simple and fast method to measure potassium and was suitable for evaluating the postmortem interval (PMI) in relatively well-preserved bodies. Sixty-two samples from medical-legal autopsies with known PMI were analyzed. A linear correlation equation for potassium concentration in the vitreous humor and PMI was established: [K(+)]=0.1702PMI+5.5678, r=0.8692.     

On-line clean-up and screening of oxacillin and cloxacillin in human urine and plasma with a weak ion exchange monolithic column

A weak ion exchange monolithic column prepared by modifying the GMA-MAA-EDMA (glycidyl methacrylate-methacrylic acid-ethylene glycol dimethacrylate) monoliths with ethylenediamine was applied to remove matrix compounds in biological fluid. Using this monolithic column, on-line clean-up and screening of oxacillin and cloxacillin in human urine and plasma samples had been investigated. Chromatography was performed by reversed-phase HPLC on a C(18) column with ultraviolet detection at 225 nm. Results showed that the ion exchange monolithic column could be used for deproteinization and retaining oxacillin and cloxacillin in human urine and plasma, which provided a simple and fast method for assaying drugs in human urine and plasma.     

Quantitative determination of azithromycin in human plasma by ultra performance liquid chromatography-electrospray ionization mass spectrometry and its application in a pharmacokinetic study

A selective, rapid and sensitive ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method was developed for the quantitative determination of azithromycin in human plasma and its application in a pharmacokinetic study. With roxithromycin as internal standard, sample pretreatment involved a one-step extraction with diethyl ether of 0.5 mL plasma. The analysis was carried out on an ACQUITY UPLC BEH C(18) column (50 mm x 2.1 mm, i.d., 1.7 microm) with gradient elution at flow rate of 0.35 mL/min. The mobile phase was 50 mM ammonium acetate and acetonitrile. The detection was performed on a triple-quadrupole tandem mass spectrometer by multiple reaction monitoring (MRM) mode via electrospray ionization (ESI). Linear calibration curves were obtained in the concentration range of 1-1000 ng/mL, with a lower limit of quantification of 1 ng/mL. The intra- and inter-day precision (RSD) values were below 15% and accuracy (RE) was -1.3% to 5.7% at all QC levels. The method was applicable to clinical pharmacokinetic study of azithromycin in healthy volunteers following oral administration.     

Fe3+ immobilized metal affinity chromatography with silica monolithic capillary column for phosphoproteome analysis

Immobilized metal affinity chromatography (IMAC) is a commonly used technique for phosphoproteome analysis due to its high affinity for adsorption of phosphopeptides. Miniaturization of IMAC column is essential for the analysis of a small amount of sample. Nanoscale IMAC column was prepared by chemical modification of silica monolith with iminodiacetic acid (IDA) followed by the immobilization of Fe3+ ion inside the capillary. It was demonstrated that Fe3+-IDA silica monolithic IMAC capillary column could specifically capture the phosphopeptides from tryptic digest of alpha-casein with analysis by MALDI-TOF MS. The silica monolithic IMAC capillary column was manually coupled with nanoflow RPLC/nanospray ESI mass spectrometer (muRPLC-nanoESI MS) for phosphoproteome analysis. The system was validated by analysis of standard phosphoproteins and then it was applied to the analysis of protein phosphorylation in mouse liver lysate. Besides MS/MS spectra, MS/MS/MS spectra were also collected for neutral loss peak. After database search and manual validation with conservative criteria, 29 singly phosphorylated peptides were identified by analyzing a tryptic digest of only 12 mug mouse liver lysate. The results demonstrated that the silica monolithic IMAC capillary column coupled with muRPLC-nanoESI MS was very suitable for the phosphoproteome analysis of minute sample.     

玉米根细胞中类整合素蛋白与α-微管蛋白的共定位及其可能的相互作用

采用间接免疫荧光标记法对玉米根细胞中的类整合素蛋白和细胞骨架主要组分之一的α-微管蛋白进行了荧光定位。结果表明：类整合素蛋白主要分布在质膜上。与对照相比,用与类整合素蛋白特异结合的5肽GRGDS处理后,质膜上类整合素的分布更为均匀,微管的排列密度降低,而用不与类整合素蛋白特异结合的GRGDS类似物SDGRG处理则对类整合素蛋白分布和微管蛋白的排列均无明显影响。微管蛋白解聚剂或稳定剂处理改变类整合素在质膜上的分布。这些结果表明类整合素蛋白与微管蛋白间有复杂的相互作用。     

小麦胚芽鞘扩展蛋白特性及对水分胁迫的响应

扩展蛋白是植物细胞壁延伸过程中的关键调节因子,在植物的生长发育以及对逆境的响应过程中起着重要作用。本文选用小麦(HF 9703)胚芽鞘为材料,采用Hepes法和SDS法分别提取小麦胚芽鞘扩展蛋白,通过改良的植物组织伸长测定仪测定其活性,并利用扩展蛋白抗体进行免疫印迹以检测其丰度,主要研究了小麦胚芽鞘扩展蛋白的特性及对水分胁迫的响应。结果表明:Hepes法提取的扩展蛋白活性较高,而SDS法的提取效率高;离体小麦胚芽鞘扩展蛋白的活性具有pH依赖性,且随缓冲液的交替更换(pH 4.5:pH 6.8)而反复逆转;扩展蛋白主要定位于细胞壁中;小麦胚芽鞘扩展蛋白和黄瓜下胚轴扩展蛋白具有交叉重组活性,但这种活性具有种属特异性。水分胁迫诱导小麦胚芽鞘扩展蛋白的活性和丰度提高,扩展蛋白活性的提高在小麦对水分胁迫的抗性方面可能具有重要作用。     

Effects of static magnetic fields on the physical and chemical properties of cell culture medium RPM1 1640

RPMI 1640 culture medium was chosen to simulate body fluids, and after exposure to 0.085 approximately 0.092 T static magnetic fields (SMF), surface tension, pH, dissolved oxygen, and UV-visible spectrum were measured. Compared with the control group in the normal geomagnetic field, the pH value increased about 0.14 units, dissolved oxygen increased about 14%, and the UV-visible spectra were different in peak intensity but without a shift in the peak. Surface tension showed no significant difference in the two groups. This data suggests that SMF can change some of the physical and chemical properties of RPM1 1640 solution, and may contribute to understanding biological effects of SMF.     

Intermolecular failure of L-type Ca2+ channel and ryanodine receptor signaling in hypertrophy

Pressure overload–induced hypertrophy is a key step leading to heart failure. The Ca²⁺-induced Ca²⁺ release (CICR) process that governs cardiac contractility is defective in hypertrophy/heart failure, but the molecular mechanisms remain elusive. To examine the intermolecular aspects of CICR during hypertrophy, we utilized loose-patch confocal imaging to visualize the signaling between a single L-type Ca²⁺ channel (LCC) and ryanodine receptors (RyRs) in aortic stenosis rat models of compensated (CHT) and decompensated (DHT) hypertrophy. We found that the LCC-RyR intermolecular coupling showed a 49% prolongation in coupling latency, a 47% decrease in chance of hit, and a 72% increase in chance of miss in DHT, demonstrating a state of “intermolecular failure.” Unexpectedly, these modifications also occurred robustly in CHT due at least partially to decreased expression of junctophilin, indicating that intermolecular failure occurs prior to cellular manifestations. As a result, cell-wide Ca²⁺ release, visualized as “Ca²⁺ spikes,” became desynchronized, which contrasted sharply with unaltered spike integrals and whole-cell Ca²⁺ transients in CHT. These data suggested that, within a certain limit, termed the “stability margin,” mild intermolecular failure does not damage the cellular integrity of excitation-contraction coupling. Only when the modification steps beyond the stability margin does global failure occur. The discovery of “hidden” intermolecular failure in CHT has important clinical implications.     

Accurate cancer classification using expressions of very few genes

We aim at finding the smallest set of genes that can ensure highly accurate classification of cancers from microarray data by using supervised machine learning algorithms. The significance of finding the minimum gene subsets is three-fold: 1) it greatly reduces the computational burden and "noise" arising from irrelevant genes. In the examples studied in this paper, finding the minimum gene subsets even allows for extraction of simple diagnostic rules which lead to accurate diagnosis without the need for any classifiers, 2) it simplifies gene expression tests to include only a very small number of genes rather than thousands of genes, which can bring down the cost for cancer testing significantly, 3) it calls for further investigation into the possible biological relationship between these small numbers of genes and cancer development and treatment. Our simple yet very effective method involves two steps. In the first step, we choose some important genes using a feature importance ranking scheme. In the second step, we test the classification capability of all simple combinations of those important genes by using a good classifier. For three "small" and "simple" data sets with two, three, and four cancer (sub)types, our approach obtained very high accuracy with only two or three genes. For a "large" and "complex" data set with 14 cancer types, we divided the whole problem into a group of binary classification problems and applied the 2-step approach to each of these binary classification problems. Through this "divide-and-conquer" approach, we obtained accuracy comparable to previously reported results but with only 28 genes rather than 16,063 genes. In general, our method can significantly reduce the number of genes required for highly reliable diagnosis