Increasing information from shotgun proteomic data by accounting for misassigned precursor ion masses

Although mass spectrometers are capable of providing high mass accuracy data, assignment of true monoisotopic precursor ion mass is complicated during data-dependent ion selection for LC-MS/MS analysis of complex mixtures. The complication arises when chromatographic peak widths for a given analyte exceed the time required to acquire a precursor ion mass spectrum. The result is that many measured monoisotopic masses are misassigned due to calculation from a single mass spectrum with poor ion statistics based on only a fraction of the total available ions for a given analyte. Such data in turn produces errors in automated database searches, where precursor m/z value is one search parameter. We propose here a postacquisition approach to correct misassigned monoisotopic m/z values that involves peak detection over the entire elution profile and correction of the precursor ion monoisotopic mass. As a result of using this approach to reprocess shotgun proteomic data we increased peptide sequence assignments by 10% while reducing the estimated false positive ratio from 1 to 0.2%. We also show that 4% of the salvaged identifications may be accounted for by correction of mixed tandem mass spectra resulting from fragmentation of multiple peptides simultaneously, a situation which we refer to as accidental CID.     

Trypsin-immobilized fiber core in syringe needle for highly efficient proteolysis

In this report, a core-changeable needle enzymatic reactor was developed for highly efficient proteolysis. A piece of enzyme-immobilized fiber core was inserted into the needle of a syringe pump to form a flow-through bioreactor. The novel in-needle bioreactor could be regenerated by changing its fiber core. The feasibility and performance of the unique bioreactor were demonstrated by the tryptic digestion of BSA and lysozyme and the digestion time was significantly reduced to less than 5 s. The digests were identified by MALDI-TOF MS with sequence coverages comparable to those obtained by the conventional in-solution tryptic digestion. The present in-needle bioreactor provides a promising platform for the high-throughput protein identification.     

彩色棉种质资源农艺性状和纤维品质鉴定与分析

基于农艺性状和纤维品质对61份彩色棉种质材料进行鉴定分析,结果表明：材料间衣分、2．5％跨长、马克隆值呈极显著差异,整齐度、伸长率、比强度和单株铃数存在显著差异,株高、果枝数、单铃重差异不显著;供试材料纤维品质较差,除中国农业科学院棉花研究所选育的棕125、棕絮1号等材料外,大部分种质系2．5％跨长、比强度等指标不能满足纺织工业的需求,但仍有31份种质系单一性状较优,如棕2—63（IAA）、棕3-944等。采用类平均法对供试材料进行聚类分析,61份材料聚为7个类群,供试材料表现型性状相似较低,尤其部分基础彩色棉遗传材料与其他材料相似性极低,单独构成一类,如皱缩红鸡角叶棕絮、hunan绿等。综合分析表明,供试材料农艺性状和纤维品质较差,遗传多样性较丰富。     

Aboveground biomass dynamics of subalpine old-growth forest in the upper reach of the Minjiang River

Biomass estimation of old-growth forests in the upper Minjiang River (UMR) is important in quantifying carbon (C) sequestration and C sink size because majority of the natural forests in UMR are mature or over-mature. Based on the forest resource data from 27 fixed sampling plots that have been surveyed consecutively, the dynamics of the aboveground biomass density (AGBD) were characterized by the allometric relationships, and the space-time variations of the C sink size in the sub-alpine old-growth forests of UMR were explored. Our results showed that 1) the net increase in AGBD was (27.311 ± 15.580) Mg·hm^?2 and the mean annual growth rate and mean annual death rate were (1.930 ± 1.091) and (2.271 ± 1.424) Mg·hm^?2·a^?1 during 1988–2002, respectively. 2) The aboveground biomass (AGB) largely depended on the growth and death rates of the trees with different diameters at the breast height (DBH) classes and the recruitment rate from one DBH class to another as well. The largest increment component of AGB came from the DBH class of 20 to 40 cm, whereas the minimum increment component of AGB was above 80 cm in DBH. The net negative increment of AGB occurred at DBH classes of 40–60 and 60–80 cm. 3) There were space-time variations of AGB in the alpine old-growth forests, indicated by AGB changing over time in the same sampling plot and varying among the locations or plots during the same sampling period. These variations were not only reflected in numerical value but also in positive or negative biomass increment.     

Monolayer Film of Phycobilisome-Thylakoid Membrane Complexes from Spirulina platensis

Monolayer films of phycobilisome-thylakoid membrane complexes isolated from Spirulina platensis were prepared at air/aqueous solution interface by using the Langmuir-Blodgett technique. The film preparation was optimized with 0.5 M phosphate buffer (pH 7.0) as sub-phase at 20 °C. The monolayer was transferred into grids and into mica surface for observing the surface image of the complexes by transmission electron microscopy and atomic force microscope, respectively. The shape of complexes was disk-like with the diameter of about 50 nm and the thickness of about 35 nm. The absorption and fluorescence spectra of the complexes in the monolayer were consistent with those in buffer solution, which suggests that the complexes in the monolayer preserve the basic functional groups of photosynthetic apparatus and can be used as a model to investigate the structural connection and functional association of the light-harvesting antenna with the reaction centres.     

利用PHI数据进行区域性植物生理信息探测与分析

本次试验研究选择两个实验区:沼泽地和植被茂盛区.利用2000年9月上旬在黑龙江省大兴安岭地区获取的推帚式超光谱成像,(PHI, pushbroom hyperspectral imager)数据进行区域性植物生理量(主要是叶绿素)的探测与生态分析.在叶绿素含量探测中,结合所获取的成像光谱PHI数据的特点,在比较不同技术方法的基础之上,选用了有效而简单可靠的RARS(Ratio analysis of reflectance spectra)指数.该色素指数与植物叶绿素a、b含量拟合的相关系数( R )达0.8以上.利用PHI数据和野外实测植物光谱分别建立沼泽地和植被茂盛区的RARS指数模式,分别得到具有指示两试验区的叶绿素a (Chl a)、叶绿素b (Chl b)以及类胡萝卜素(Cars)的参数图像.更进一步地利用Blackburn(1998)所建立的RARS指数与叶绿素浓度之间的强拟合方程,相对定量估算了叶绿素a、b浓度的区域性分布,清晰地反映出植被生态状况和差异.这与野外实地考察较为一致.     

米心水青冈幼苗对光照和养分的响应

在模拟郁闭林下(L1,大约1%~2%的全日照)、林窗(L2,大约18%的全日照)、开阔地(L3,全日照)3个光照水平和每个光照水平下进行施肥(F1)和不施肥(F0)对照的6个实验处理条件下,研究了2年龄米心水青冈(FagusenglerianaSeem)幼苗在随后的两个生长季里的生长对光照和土壤养分的响应。结果显示:光照和养分对幼苗高度、基径和生物量有显著的影响。经过两个生长季,L1处理下幼苗高度增量极显著地小于L2和L3处理下幼苗高度增量。L1处理下基径和生物量的增量在处理当年秋就极显著地小于L2和L3处理下的增量,并在第二年差异继续扩大。L2和L3处理下的幼苗间的生长没有显著差异。施肥明显地促进了L2和L3处理下的幼苗的生长,但对L1处理下的幼苗没有明显的作用。这些结果说明,虽然2年龄米心水青冈幼苗能够在林下的弱光条件下生存,但生长受到了极大的抑制。幼苗在林窗的中等光照条件下能够与在开阔地全日照条件下生长的一样好或更好,这与许多耐阴的落叶树的响应一样。在比林内光照强度较高的条件下施肥或较高的土壤养分才对米心水青冈幼苗的生长和生存起作用。     

Spectroscopic Investigation of the Interaction Between Copper (II) 2-oxo-propionic Acid Salicyloyl Hydrazone Complex and Bovine Serum Albumin

The interaction between copper (II) 2-oxo-propionic acid salicyloyl hydrazone (Cu^IIL) and bovine serum albumin (BSA) under physiological conditions was investigated by the methods of fluorescence spectroscopy, UV-Vis absorption, and circular dichroism spectroscopy. Fluorescence data showed that the fluorescence quenching of BSA by Cu^IIL was the result of the formation of the BSA–Cu^IIL complex. The apparent binding constants (K _a) between Cu^IIL and BSA at four different temperatures were obtained according to the modified Stern–Volmer equation. The thermodynamic parameters, enthalpy change (ΔH) and entropy change (ΔS), for the reaction were calculated to be ?80.79 kJ mol^?1 and ?175.48 J mol^?1 K^?1 according to van’t Hoff equation. The results indicated that van der Waals force and hydrogen bonds were the dominant intermolecular force in stabilizing the complex. The binding distance (r) between Cu^IIL and the tryptophan residue of BSA was obtained to be 4.1 nm according to Förster’s nonradioactive energy transfer theory. The conformational investigation showed that the application of Cu^IIL increased the hydrophobicity of amino acid residues and decreased the α-helical content of BSA (from 62.71% to 37.31%), which confirmed some microenvironmental and conformational changes of BSA molecules.     

Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm

The narrow genetic base of cultivated cotton germplasm is hindering the cotton productivity worldwide. Although potential genetic diversity exists in Gossypium genus, it is largely ‘underutilized’ due to photoperiodism and the lack of innovative tools to overcome such challenges. The application of linkage disequilibrium (LD)-based association mapping is an alternative powerful molecular tool to dissect and exploit the natural genetic diversity conserved within cotton germplasm collections, greatly accelerating still ‘lagging’ cotton marker-assisted selection (MAS) programs. However, the extent of genome-wide linkage disequilibrium (LD) has not been determined in cotton. We report the extent of genome-wide LD and association mapping of fiber quality traits by using a 95 core set of microsatellite markers in a total of 285 exotic Gossypium hirsutum accessions, comprising of 208 landrace stocks and 77 photoperiodic variety accessions. We demonstrated the existence of useful genetic diversity within exotic cotton germplasm. In this germplasm set, 11–12% of SSR loci pairs revealed a significant LD. At the significance threshold (r² ≥ 0.1), a genome-wide average of LD declines within the genetic distance at < 10 cM in the landrace stocks germplasm and > 30 cM in variety germplasm. Genome wide LD at r² ≥ 0.2 was reduced on average to  1–2 cM in the landrace stock germplasm and 6–8 cM in variety germplasm, providing evidence of the potential for association mapping of agronomically important traits in cotton. We observed significant population structure and relatedness in assayed germplasm. Consequently, the application of the mixed liner model (MLM), considering both kinship (K) and population structure (Q) detected between 6% and 13% of SSR markers associated with the main fiber quality traits in cotton. Our results highlight for the first time the feasibility and potential of association mapping, with consideration of the population structure and stratification existing in cotton germplasm resources. The number of SSR markers associated with fiber quality traits in diverse cotton germplasm, which broadly covered many historical meiotic events, should be useful to effectively exploit potentially new genetic variation by using MAS programs.     

Adipose triglyceride lipase (ATGL) expression in human skeletal muscle is type I (oxidative) fiber specific

Accumulation of triacylglycerol (TAG) and lipid intermediates in skeletal muscle plays an important role in the etiology of insulin resistance and type 2 diabetes mellitus. Disturbances in skeletal muscle lipid turnover and lipolysis may contribute significantly to this. So far, knowledge on the regulation of muscle lipolysis is limited. Recently the identification of a new lipase was reported: adipose triglyceride lipase (ATGL). ATGL deficient animals show significant lipid accumulation in skeletal muscle, which may indicate that ATGL plays a pivotal role in skeletal muscle lipolysis. However, until now, it is still unknown whether ATGL protein is expressed in human skeletal muscle. Therefore, the aim of the present study was to investigate whether ATGL is expressed at the protein level in human skeletal muscle, and to examine whether its expression is fiber-type specific. To accomplish this, we established an imunohistochemical and immunofluorescent staining procedure to study ATGL protein expression in relation to fiber type in human vastus lateralis muscle of eight male subjects (BMI range: 21.0–34.5 kg/m² and age: 38–59 years). In the present paper we report for the first time that ATGL protein is indeed expressed in human skeletal muscle. Moreover, ATGL is exclusively expressed in type I (oxidative) muscle fibers, suggesting a pivotal role for ATGL in intramuscular fatty acid handling, lipid storage and breakdown.