Large-scale Identification of N-linked Intact Glycopeptides in Human Serum using HILIC Enrichment and Spectral Library Search

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Highlights

• •This study proposed a spectral library search method to accurately identify N-linked glycopeptides in human serum through LC-MS/MS with pMatchGlyco software.
• •The identification depth of serum N-linked intact glycopeptides and glycoproteins was increased by combination of acetonitrile precipitation, HILIC enrichment and high-pH RPLC fractionation.
• •22,677 unique serum N-linked intact glycopeptides corresponding to 526 N-linked glycoproteins were identified with N-glycosylation motif-specific FDR control.
• •This study revealed the great microheterogeneity of N-linked glycoproteins in serum.

     

Where Is the Site of the “Oxygen Burst” Located During Light Induction in Dark-Adapted Leaves？ A Study Using Photoacoustic Techniques

The “oxygen burst” phenomenon that appeared during the light-induction period of intact leaves could be monitored using a photoacoustic technique high time resolution. The relationship between oxygen bursts and dark-adapted time, far-red light pretreatment, photothermal signal, and chlorophyll a (Ch1 a) fluorescence kinetics were investigated in the present study. Using extraneous inhibitors or cofactors of electron transport, a modified vacuum-infiltration method was undertaken to locate directly the site at which oxygen bursts of intact leaves occurred. We found that the photothermal signal showed little evidence of oscillation during the light-induction period. The oxygen burst was resolved into two components if darkadapted time lasted longer than 20 min. Methyl viologen (MV) or far-red light could not eliminate the first component, whereas formate-Na (pH 7.0, 20μmol/L) eliminated the first component but had no effect on the second one. Furthermore, the photochemical quenching, the electron transport rate of Chl a fluorescence,and the first component of the oxygen bursts approached lowest values simultaneously. This evidence indicates that the site at which the first component of oxygen bursts occurred was located between photosystem (PS)I and PSII (i.e. the PQ pool). The formate-Na experiment also showed a linkage between the first component and the S state of oxygen evolution at the donor side of PSII. Furthermore, elimination of the second component by far-red light and absorption of the second component by MV indicated that the site at which the second component of oxygen bursts may be located at the acceptor side of PSII.     

POINT technology illuminates the processing of polymerase-associated intact nascent transcripts

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Redox-responsive in vitro modulation of the signalling state of the isolated PrrB sensor kinase of Rhodobacter sphaeroides NCIB 8253

Prr is a global regulatory system that controls a large and diverse range of genes in Rhodobacter sphaeroides in response to changing conditions of environmental redox potential. PrrB is the membrane-bound sensor kinase and previously we showed that the purified, detergent-solubilised intact membrane protein is functional in autophosphorylation, phosphotransfer and phosphatase activities. Here we confirm that it also senses and responds directly to its environmental signal, redox potential; strong autophosphorylation of PrrB occurred in response to dithiothreitol (DTT)-induced reducing conditions (and levels increased in response to a wide 0.1-100 mM DTT range), whilst under oxidising conditions, PrrB exhibited low, just detectable levels of autophosphorylation. The clear response of PrrB to changes in reducing conditions confirmed its suitability for in vitro studies to identify modulators of its phosphorylation signalling state, and was used here to investigate whether PrrB might sense more than one redox-related signal, such as signals of cell energy status. NADH, ATP and AMP were found to exert no detectable effect on maintenance of the PrrB-P signalling state. By contrast, adenosine diphosphate produced a very strong increase in PrrB-P dephosphorylation rate, presumably through the back-conversion of PrrB-P to PrrB.     

用伊文思蓝染色法检测植物整体叶片的细胞活性

本文利用伊丈思蓝（evans blue）作为细胞活性染料,检测了胁迫处理后3种草本和2种灌木植物叶片的细胞活性。结果显示,不同类型的胁迫（温度、PEG、Pb、Cd、NaCl和NaHSO3）均造成了叶片细胞一定程度的伤害。随着各种胁迫的加剧,叶片染色面积和染色后提取液吸光度都呈现梯度增加的趋势。研究分别利用染色面积和其提取液吸光度表达叶片细胞的活性,提出了一种更安全、更准确的植物整体叶片细胞活性检测方法。     

Control of Na+ and K+ transport in Spergularia marina I. Transpiration effects

In this paper we begin our study of factors controlling Na⁺ and K⁺ uptake in the halophyte Spergularia marina (L.) Griseb., with emphasis on plants growing at moderate salinity (0.2x sea water). The involvement of transpiration was considered first because of its potential to account for much or all of the transport of ions, and particularly of Na⁺, to the shoot under these growth conditions. Transpiration was constant with time through most of the light period, quickly dropping to 6% of the day time rate at night. ²²Na⁺ uptake, on the other hand, showed much less day/night variation, and relative transport to the shoot was constant. After establishing that transpiration was linearly related to leaf weight, possible transpiration effects were further considered as correlations between leaf weight and transport to the shoot. Under constant, day-time conditions, with linear effects of time and plant size removed, total transport of ²²Na⁺ to the shoot (per plant) was not correlated to leaf weight. A similar result was found when transport was expressed per gram of root, and when partitioning of total label to the shoot was considered. Finally, the correlation was considered between leaf weight and a Na⁺/K⁺ enrichment factor defined as the Na⁺/K⁺ ratio in the leaves divided by that in the roots. This correlation was also insignificant. The results indicate that analysis of control of Na⁺ and K⁺ uptake and transport in this experimental system need not consider effects of transpiration.     

Dependence of energization of thylakoids on frequency of exciting flashes in intact chloroplasts

We investigated the frequency-dependence of the flash-induced electrochromic absorbance change, A₅₁₅, and of the pH-indicating absorbance change of neutral red in isolated intact chloroplasts. The energization pattern of thylakoids depended strongly on the frequency (f) of the exciting flashes, tested between 0.05 and 2 s^–1. When the frequency was increased from 0.1 to 1 s^–1 the total initial change and the slow rise of A₅₁₅ decreased by about 30% and 70%, respectively, and both the slow rise and decay were considerably accelerated. These changes were fully reversible, even after prolonged excitation at 1 s^–1, if the frequency was decreased again to 0.1 s^–1. Accumulation of an appreciable transmembrane electric field strength could not be detected in any of our experiments, at high frequency, since the decay of A₅₁₅ was considerably accelerated when the frequency was increased. In contrast, pH significantly increased at higher frequencies of the exciting flashes. In the steady-state (after about 100 flashes) pH was about 0.5–0.8 pH unit higher than in the dark or at low frequencies. In the presence of nigericin or dithionite, both of which prevented accumulation of protons in the lumen, the total initial change in A₅₁₅ at f=1 s^–1 relative to that at f=0.1 s^–1 decreased to a similar extent as in the control. The proportion of the slow rise relative to the initial amplitude, however, did not decrease. Our data support the suggestion that pH controls the amplitude of the slow rise of A₅₁₅. However, contrary to a previous statement (B. Bouges-Bouquet (1981) Biochim. Biophys. Acta 535, 327–340), we show that the pH effect cannot be accounted for by variation of the rate of this kinetic component of A₅₁₅.Abbreviations DCMU 3(3,4-dichlorophenyl)-1,1-dimethylurea - f frequency of the exciting flashes - HEPES N-2-hydroxyethylpiperazine-N-2-ethanesulfonic acid - PS photosystem     

Effect of ethylene antagonists on auxin-induced inhibition of intact primary root elongation in maize (Zeamays L.)

We tested that the hypothesis that root elongation might be controlled by altering the level of ethylene in intact primary roots of maize(Zea mays L.). We measured root elongation in a short period using a computerized root auxanometer. Compounds which regulate ethylene production were applied to intact primary roots in different time periods. Root elongation was stimulated by the treatment with ethylene antagonists such as Co²⁺, aminoethoxyvinylglycine (AVG) and L-canaline. This result suggested that root elongation was closely related to ethylene level of intact primary roots. Furthermore, IAA- and 1-aminocyclopropane-1-carboxylic acid (ACC)-induced inhibition of root elongation was reversed by treatment with Co²⁺. The application of ACC to roots which have been exposed to IAA and Co²⁺ have no significant effect on root elongation. However, the inhibition of root elongation by ACC in roots previously treated with IAA and AVG became manifest when the applied IAA concentrations were lower. These results were consistent with the hypothesis that the level of ethylene in intact roots functions to moderate root elongation, and suggested that auxin-induced inhibition of root elongation results from auxin induced promotion of ethylene production.     

Crystallization of intact monoclonal antibodies

Attempts were made to crystallize four monoclonal antibodies, one IgG_2ak and three IgG_1k. Using a PEG 3350 screen combined with detergents, and developed from our experiments with an IgG_2ak antibody specific for canine lymphoma cells,^1,2 crystals have now been obtained of two of these four immunoglobulins, an antiphenytoin and an antiphenobarbital antibody. A complex between the antiphenobarbital antibody and its drug antigen crystallized as well. The antibody for phenytoin has, to this point, produced only clustered microcrystals, marginally suitable for X-ray analysis. Single crystals of the IgG_1k antibody against phenobarbital, however, were characterized by X-ray diffraction to be primitive monoclinic, with unit cell dimensions a = 67 Å, b = 193 Å, c = 74 Å, and β = 110°. These crystals have an entire IgG_1k molecule as the asymmetric unit and they diffract to at least 3.2 Å resolution. © 1995 Wiley-Liss, Inc.