SELDI-TOF-MS筛选慢性阻塞性肺疾病血清标志蛋白的初步研究

目的:利用表面增强激光解吸电离飞行时间质谱技术(SELDI-TOF-MS)筛选慢性阻塞性肺疾病(COPD)血清特异标志物。方法:应用SELDI-TOF-MS技术检测30例COPD稳定期患者和30例健康对照者血清蛋白指纹图谱,采用Biomarker pattern软件进行分析,建立COPD的诊断模型。结果:COPD患者血清蛋白图谱与对照组相比,在相对分子质量2000-15 000范围内共检测到75个蛋白峰,发现19个有统计学差异的蛋白峰(P0.05)。通过对COPD组与对照组间的数据作进一步分析,经BPS软件分析,建立质荷比(M/Z)3 167、4 645的差异蛋白组成的诊断模型,其诊断敏感度为96.67%,特异度为96.67%。结论:SELDI-TOF-MS技术是一种快速、简单易行、用量少和高通量的分析方法。能直接筛选出COPD血清中特异表达标志物,用特异表达标志物建立的诊断模型能有效区分COPD患者与健康对照者,有望成为COPD诊断的辅助指标。     

Effect of deamidation on folding of ribonuclease A

The folding of ribonuclease A (RNase A) has been extensively studied by characterizing the disulfide containing intermediates using different experimental conditions and analytical techniques. So far, some aspects still remain unclear such as the role of the loop 65-72 in the folding pathway. We have studied the oxidative folding of a RNase A derivative containing at position 67 the substitution Asn --> isoAsp where the local structure of the loop 65-72 has been modified keeping intact the C65-C72 disulfide bond. By comparing the folding behavior of this mutant to that of the wild-type protein, we found that the deamidation significantly decreases the folding rate and alters the folding pathway of RNase A. Results presented here shed light on the role of the 65-72 region in the folding process of RNase A and also clarifies the effect of the deamidation on the folding/unfolding processes. On a more general ground, this study represents the first characterization of the intermediates produced along the folding of a deamidated protein.     

A possible role of alanine for ammonia transfer between astrocytes and glutamatergic neurons

The metabolism of [U-(13)C]lactate (1 mM) in the presence of unlabeled glucose (2.5 mM) was investigated in glutamatergic cerebellar granule cells, cerebellar astrocytes, and corresponding co-cultures. It was evident that lactate is primarily a neuronal substrate and that lactate produced glycolytically from glucose in astrocytes serves as a substrate in neurons. Alanine was highly enriched with (13)C in the neurons, whereas this was not the case in the astrocytes. Moreover, the cellular content and the amount of alanine released into the medium were higher in neurons than astrocytes. On incubation of the different cell types in medium containing alanine (1 mM), the astrocytes exhibited the highest level of accumulation. Altogether, these results indicate a preferential synthesis and release of alanine in glutamatergic neurons and uptake in cerebellar astrocytes. A new functional role of alanine may be suggested as a carrier of nitrogen from glutamatergic neurons to astrocytes, a transport that may operate to provide ammonia for glutamine synthesis in astrocytes and dispose of ammonia generated by the glutaminase reaction in glutamatergic neurons. Hence, a model of a glutamate-glutamine/lactate-alanine shuttle is presented. To elucidate if this hypothesis is compatible with the pattern of alanine metabolism observed in the astrocytes and neurons from cerebellum, the cells were incubated in a medium containing [(15)N]alanine (1 mM) and [5-(15)N]glutamine (0.5 mM), respectively. Additionally, neurons were incubated with [U-(13)C]glutamine to estimate the magnitude of glutamine conversion to glutamate. Alanine was labeled from [5-(15)N]glutamine to 3.3% and [U-(13)C]glutamate generated from [U-(13)C]glutamine was labeled to 16%. In spite of the modest labeling in alanine, it is clear that nitrogen from ammonia is transferred to alanine via transamination with glutamate formed by reductive amination of alpha-ketoglutarate. With regard to the astrocytic part of the shuttle, glutamine was labeled to 22% in one nitrogen atom whereas 3.2% was labeled in two when astrocytes were incubated in [(15)N]alanine. Moreover, in co-cultures, [U-(13)C]alanine labeled glutamate and glutamine equally, whereas [U-(13)C]lactate preferentially labeled glutamate. Altogether, these results support the role proposed above of alanine as a possible ammonia nitrogen carrier between glutamatergic neurons and surrounding astrocytes and they show that lactate is preferentially metabolized in neurons and alanine in astrocytes.     

Initiating Events in Direct Cardiomyocyte Reprogramming

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Toward a high resolution 2-DE profile of the normal human liver proteome using ultra-zoom gels

The human liver is the largest organ in the body and has many important physiological functions. A global analysis of human liver proteins is essential for a better understanding of the molecular basis of the normal functions of the liver and of its diseases. As part of the Human Liver Proteome Project (HLPP), the goal of the present study was to visualize and detect as many proteins as possible in normal human livers using two-dimensional gel electrophoresis (2-DE). We have constructed a reference map of the proteins of human normal liver that can be used for the comprehensive analysis of the human liver proteome and other related research. To improve the resolution and enhance the detection of low abundance proteins, we developed and optimized narrow pH range ultra-zoom 2-DE gels. High resolution patterns of human liver in pH gradients 4.5–5.5, 5–6, 5.5–6.7, 6–9 and 6–11 are presented. To improve the poor resolution in the alkaline pH range of 2-DE gels, we optimized the isoelectric focusing protocol by including sample application using cup loading at the anode and incorporating 1.2% hydroxyethyl disulfide, 15% 2-propanol and 5% glycerol in the rehydration buffer. Using the optimized protocol, we obtained reproducibly better resolution in both analytical and preparative 2-DE gels. Compared with the 2386 and 1878 protein spots resolved in the wide range 3–10 and 4–7 pH gradients respectively, we obtained 5481 protein spots from the multiple (overlapping) narrow pH range ultra-zoom gels in the range of pH 4.5–9. The visualized reference map of normal human liver proteins presented in this paper will be valuable for comparative proteomic research of the liver proteome.     

Allometric deviations of plasma carotenoids in raptors

Because large species ingest proportionally less food than small ones, it may be predicted that they should incorporate relatively fewer carotenoids to a proportionally equal volume of blood. However, some species may increase their levels of circulating carotenoids by ingesting unusual food. We tested whether the plasma concentration of carotenoids scales to the three‐quarter power of mass in nine predatory and scavenger raptor species. No significant allometric relationships were found due to the unusually high concentrations of carotenoids in the Egyptian Vulture Neophron percnopterus and the Andean condor Vultur gryphus. To assess whether these two species deviate from the allometric rule through the exploitation of unusual sources of carotenoids, or due to a physiological adaptation to improve the uptake of carotenoids, we determined allometric patterns in individuals of these two species kept in captivity with an exclusive diet of flesh. Our results provided support for the allometric rule because the slope of the allometric equation did not differ from a three‐quarter exponent when carotenoid levels of the two outliers were replaced by those of captive birds. This adjustment to the allometric rule suggests a lack of any physiological adaptation to improve the uptake of the low concentrations of carotenoids contained in flesh. Differences between species in carotenoid incorporation into the bloodstream may be ultimately due to contrasting evolutionary history, physiology and associated colour‐signalling strategies, but proximately due to the acquisition of these micronutrients from both usual and unusual dietary sources.     

Structural elucidation of phosphoglycolipids from strains of the bacterial thermophiles Thermus and Meiothermus

The structures of two major phosphoglycolipids from the thermophilic bacteria Thermus oshimai NTU-063, Thermus thermophilus NTU-077, Meiothermus ruber NTU-124, and Meiothermus taiwanensis NTU-220 were determined using spectroscopic and chemical analyses to be 2'-O-(1,2-diacyl-sn-glycero-3-phospho) -3'-O-(alpha-N-acetyl-glucosaminyl)-N-glyceroyl alkylamine [PGL1 (1)] and the novel structure 2'-O-(2-acylalkyldio-1-O-phospho)-3'-O-(alpha-N-acetylglucosaminyl)-N-glyceroyl alkylamine [PGL2 (2)]. PGL2 (2) is the first phosphoglycolipid identified with a 2-acylalkyldio-1-O-phosphate moiety. The fatty acids of the phosphoglycolipids are mainly iso-C(15:0), -C(16:0), and -C(17:0) and anteiso-C(15:0) and -C(17:0). The ratios of PGL2 (2) to PGL1 (1) are significantly altered when grown at different temperatures for three strains, T. thermophilus NTU-077, M. ruber NTU-124, and M. taiwanensis NTU-220, but not for T. oshimai NTU-063. Accordingly, the ratios of iso- to anteiso-branched fatty acids increase when grown at the higher temperature.     

kLa of stirred tank bioreactors revisited

By means of improved feedback control k_La measurements become possible at a precision and reproducibility that now allow a closer look at the influences of power input and aeration rate on the oxygen mass transfer. These measurements are performed online during running fermentations without a notable impact on the biochemical conversion processes. A closer inspection of the mass transfer during cultivations showed that at least the number of impellers influences mass transfer and mixing: On the laboratory scale, two hollow blade impellers clearly showed a larger k_La than the usually employed three impeller versions when operated at the same agitation power and aeration rate. Hollow blade impellers are preferable under most operational conditions because of their perfect gas handling capacity. Mixing time studies showed that these two impeller systems are also preferable with respect to mixing. Furthermore the widths of the baffle bars depict a significant influence on the k_La. All this clearly supports the fact that it is not only the integral power density that finally determines k_La.     

An immunoaffinity purification method for the proteomic analysis of ubiquitinated protein complexes

Protein ubiquitination plays an important role in the regulation of many cellular processes, including protein degradation, cell cycle regulation, apoptosis, and DNA repair. To study the ubiquitin proteome we have established an immunoaffinity purification method for the proteomic analysis of endogenously ubiquitinated protein complexes. A strong, specific enrichment of ubiquitinated factors was achieved using the FK2 antibody bound to protein G-beaded agarose, which recognizes monoubiquitinated and polyubiquitinated conjugates. Mass spectrometric analysis of two FK2 immunoprecipitations (IPs) resulted in the identification of 296 FK2-specific proteins in both experiments. The isolation of ubiquitinated and ubiquitination-related proteins was confirmed by pathway analyses (using Ingenuity Pathway Analysis and Gene Ontology-annotation enrichment). Additionally, comparing the proteins that specifically came down in the FK2 IP with databases of ubiquitinated proteins showed that a high percentage of proteins in our enriched fraction was indeed ubiquitinated. Finally, assessment of protein–protein interactions revealed that significantly more FK2-specific proteins were residing in protein complexes than in random protein sets. This method, which is capable of isolating both endogenously ubiquitinated proteins and their interacting proteins, can be widely used for unraveling ubiquitin-mediated protein regulation in various cell systems and tissues when comparing different cellular states.     

Postnatal growth in the Long-fingered Bat,Miniopterus schreibersii pallidus,in Iran (Chiroptera: Miniopteridae)

This study describes the postnatal development of body mass, forearm length and epiphyseal phalangeal gap in a free ranging population of the Long-fingered Bat, Miniopterus schreibersii pallidus Thomas, 1907, in a maternity roost in the Mahidasht cave in western Iran. The pups at birth had a mean body mass of 3.74?±?0.09 g and forearm length of 24.3?±?0.31mm. The length of forearm and body mass increased linearly during first two weeks, and thereafter maintained an apparent stability. The epiphyseal gap of the fourth metacarpal phalangeal joint increased until the thirteenth day, then decreased linearly until the 70th day and thereafter fused. The rate of body mass gain and forearm growth during the first 13 days was 0.54 g/day and 1.39 mm/day, respectively. Initiation of flight occurred three weeks after birth. A method of estimating age was derived from the values of the forearm length and the total gap of the fourth metacarpal-phalangeal joint during the pre-flight and post-flight periods.