Rat plasma proteomics: effects of abundant protein depletion on proteomic analysis

The proteomic analysis of plasma and serum samples represents a formidable challenge due to the presence of a few highly abundant proteins such as albumin and immunoglobulins. Detection of low abundance protein biomarkers requires therefore either the specific depletion of high abundance proteins with immunoaffinity columns and/or optimized protein fractionation methods based on charge, size or hydrophobicity. Here we describe the depletion of seven abundant rat plasma proteins with an immunoaffinity column with coupled antibodies directed against albumin, IgG, transferrin, IgM, haptoglobin, fibrinogen and alpha1-anti-trypsin. The IgY-R7-LC2 (Beckman Coulter) column showed high specificity for the targeted proteins and was able to efficiently remove most of the albumin, IgG and transferrin from rat plasma samples as judged by Western blot analysis. Depleted rat plasma protein samples were analyzed by SELDI-TOF MS, 2D SDS-PAGE and 2D-LC and compared to non-depleted plasma samples as well as to the abundant protein fraction that was eluted from the immunoaffinity column. Analysis of the depleted plasma protein fraction revealed improved signal to noise ratios, regardless of which proteomic method was applied. However, only a small number of new proteins were observed in the depleted protein fraction. Immunoaffinity depletion of abundant plasma proteins results in the significant dilution of the original sample which complicates subsequent analysis. Most proteomic approaches require specialized sample preparation procedures during which significant losses of less abundant proteins and potential biomarkers can occur. Even though abundant protein depletion reduces the dynamic range of the plasma proteome by about 2-3 orders of magnitude, the difference between medium-abundant and low abundant plasma proteins is still in the range of 7-8 orders of magnitude and beyond the dynamic range of current proteomic technologies. Thus, exploring the plasma proteome in greater detail remains a daunting task.     

Serum IGF-1 affects skeletal acquisition in a temporal and compartment-specific manner

Insulin-like growth factor-1 (IGF-1) plays a critical role in the development of the growing skeleton by establishing both longitudinal and transverse bone accrual. IGF-1 has also been implicated in the maintenance of bone mass during late adulthood and aging, as decreases in serum IGF-1 levels appear to correlate with decreases in bone mineral density (BMD). Although informative, mouse models to date have been unable to separate the temporal effects of IGF-1 depletion on skeletal development. To address this problem, we performed a skeletal characterization of the inducible LID mouse (iLID), in which serum IGF-1 levels are depleted at selected ages. We found that depletion of serum IGF-1 in male iLID mice prior to adulthood (4 weeks) decreased trabecular bone architecture and significantly reduced transverse cortical bone properties (Ct.Ar, Ct.Th) by 16 weeks (adulthood). Likewise, depletion of serum IGF-1 in iLID males at 8 weeks of age, resulted in significantly reduced transverse cortical bone properties (Ct.Ar, Ct.Th) by 32 weeks (late adulthood), but had no effect on trabecular bone architecture. In contrast, depletion of serum IGF-1 after peak bone acquisition (at 16 weeks) resulted in enhancement of trabecular bone architecture, but no significant changes in cortical bone properties by 32 weeks as compared to controls. These results indicate that while serum IGF-1 is essential for bone accrual during the postnatal growth phase, depletion of IGF-1 after peak bone acquisition (16 weeks) is compartment-specific and does not have a detrimental effect on cortical bone mass in the older adult mouse.     

葛藤节肢动物类群结构动态

本文利用群落结构的有关指数(物种数S、丰富度指数R、多样性指数H、H'、D和DMc、均匀性指数J'、优势度指数d和优势集中性指数C)分析了葛藤节肢动物类群结构变化动态.结果表明,葛藤节肢动物类群丰富度和多样性一年中出现两个高峰,一个在五月下旬,一个在十一月上中旬,在第一个峰期,S,R,D,H',H和DMc的值依次为38.00,6.0205,0.9056,4.0205,3.8560和0.7207,在第二个峰期,上述指数依次为34.00,6.6661,0.9245,4.2124,3.6779和0.7808;均匀性在一至四月变化较剧烈,最大值0.8899出现在1月中旬,最小值0.5765出现在二月下旬,其它时间较为平稳;优势集中性和优势度指数的变化趋势一致,其高峰值出现在二月下旬至三月上旬.分析表明,多样性和优势集中性变化趋势往往相反,即物种越丰富,多样性越大,相应的优势集中性就越小,反之就大;均匀性与多样性关系密切,即群落多样性较高时均匀度变化较为平稳,反之,就剧烈.     

Metabolic profiling of serum using Ultra Performance Liquid Chromatography and the LTQ-Orbitrap mass spectrometry system

Advances in analytical instrumentation can provide significant advantages to the volume and quality of biological knowledge acquired in metabolomic investigations. The interfacing of sub-2mum liquid chromatography (UPLC ACQUITY((R))) and LTQ-Orbitrap mass spectrometry systems provides many theoretical advantages. The applicability of the interfaced systems was investigated using a simple 11-component metabolite mix and a complex mammalian biofluid, serum. Metabolites were detected in the metabolite mix with signals that were linear with their concentration over 2.5-3.5 orders of magnitude, with correlation coefficients greater than 0.993 and limits of detection less than 1mumolL(-1). Reproducibility of retention time (RSD<3%) and chromatographic peak area (RSD<15%) and a high mass accuracy (<2ppm) were observed for 14 QC serum samples interdispersed with other serum samples, analysed over a period of 40h. The evaluation of a single deconvolution software package (XCMS) was performed and showed that two parameters (snthresh and bw) provided significant changes to the number of peaks detected and the peak area reproducibility for the dataset used. The data were used to indicate possible biomarkers of pre-eclampsia and showed both the instruments and XCMS to be applicable to the reproducible and valid detection of disease biomarkers present in serum.     

On-line coupling of size exclusion chromatography and capillary electrophoresis via solid-phase extraction and a Tee-split interface

An on-line size exclusion chromatography (SEC)-solid-phase extraction (SPE)-capillary electrophoresis (CE) system using a Tee-split interface has been developed for the analysis of peptides in biological fluids. The SEC column fractionates the sample by molecular size and the low-molecular-weight fraction, which contains the peptides, is directed to a C(18) SPE microcolumn, where the peptides are trapped and concentrated. The SPE column is desorbed with 425 nL acetonitrile and the effluent is sent to the Tee-split interface, which hydrodynamically splits (1:40) the flow and, thus, allows appropriate injection of analytes into the CE system. The performance of the system is investigated by the analysis of enkephalins in cerebrospinal fluid (CSF). It is demonstrated that the SEC step efficiently removes potentially interfering proteins, permitting reproducible SPE and CE. The total system provides efficient separations of the enkephalins with plate numbers up to 100,000. Concentration limits of detection (S/N = 3) for the peptides are about 100 ng/mL for injection of 20 microL spiked CSF samples. Plots of enkephalin peak areas versus concentration showed good linearity over the 0.25-10 microg/mL range (R2 > or = 0.985). Repeatability of migration time and peak area was within 2% and 10% R.S.D., respectively.     

A novel peak detection approach with chemical noise removal using short‐time FFT for prOTOF MS data

Peak detection is a pivotal first step in biomarker discovery from MS data and can significantly influence the results of downstream data analysis steps. We developed a novel automatic peak detection method for prOTOF MS data, which does not require a priori knowledge of protein masses. Random noise is removed by an undecimated wavelet transform and chemical noise is attenuated by an adaptive short‐time discrete Fourier transform. Isotopic peaks corresponding to a single protein are combined by extracting an envelope over them. Depending on the S/N, the desired peaks in each individual spectrum are detected and those with the highest intensity among their peak clusters are recorded. The common peaks among all the spectra are identified by choosing an appropriate cut‐off threshold in the complete linkage hierarchical clustering. To remove the 1 Da shifting of the peaks, the peak corresponding to the same protein is determined as the detected peak with the largest number among its neighborhood. We validated this method using a data set of serial peptide and protein calibration standards. Compared with MoverZ program, our new method detects more peaks and significantly enhances S/N of the peak after the chemical noise removal. We then successfully applied this method to a data set from prOTOF MS spectra of albumin and albumin‐bound proteins from serum samples of 59 patients with carotid artery disease compared to vascular disease‐free patients to detect peaks with S/N≥2. Our method is easily implemented and is highly effective to define peaks that will be used for disease classification or to highlight potential biomarkers.     

Cyclic nucleotide phosphodiesterase activities from pig coronary arteries. Lack of interconvertibility of major forms

DEAE-cellulose chromatography, with or without dithiothreitol and over a pH range of 6.0 to 8.5, resolved two phosphodiesterase activities (peaks I and II) from the soluble fraction of pig coronary arteries. The activity of peak I was increased by calmodulin (3-7-fold), whereas that of peak II was not. Chromatography of peak I on Biol-Gel A-0.5 m columns resolved two peaks of phosphodiesterase activity (peaks Ia and Ib). Peak Ia was eluted in the presence or absence of 0.1 M KCl and was relatively insensitive to calmodulin. Peak Ib was eluted only in the presence of KCl and was sensitive to calmodulin. The substrate specificity and kinetic behavior were the same for peaks I, Ia, and Ib. Repeated gel chromatography of either peak Ia or Ib, under appropriate conditions, yielded a mixture of peaks Ia and Ib. Peak Ia appears to be a reversible aggregate of peak Ib. Gel chromatography of peak II resolved only one phosphodiesterase activity, which was eluted without KCl, was highly specific for cyclic AMP, was not sensitive to calmodulin and migrated differently on the gel column than either peak Ia or Ib. Sucrose density gradient centrifugation of the soluble fraction from pig coronary arteries in the presence or absence of dithiothreitol resolved two peaks of phosphodiesterase activity (6.6 S and 3.6 S) which were similar to peaks I and II separated by DEAE-cellulose chromatography with regard to their substrate specificity and their sensitivity to calmodulin. Upon recentrifugation, each of the two peaks of phosphodiesterase activity gave a single peak of activity which migrated with the same S value as did its parent. These results indicate that the two major forms of phosphodiesterase of pig coronary arteries, which are representative of those found in many tissues, are not interconvertible in cell-free systems.     

Effects of cholesterol feeding on primate serum lipoproteins. III. The change in high density lipoprotein components

Sooty mangabey (Cercocebus atys) monkeys had a lower serum HDL cholesterol concentration than any other Old World monkey species reported. In addition, they had a higher serum Lp(a) concentration than other species. The mangabeys were fed a cholesterol-fat diet for 5 weeks. HDL2 and HDL3 amounts were determined from the two peaks apparent upon analytical ultracentrifugation. In the first 1-3 weeks, 13 of the 14 mangabeys increased 30% (mean) in total HDL, this increase occurring only in the HDL2 fraction. After 5 weeks, HDL and HDL2 decreased markedly. During the cholesterol feeding, HDL3 continually decreased in flotation rate, indicating it was either smaller and/or denser. HDL2 and HDL3 separated well on molecular sieving agarose columns during the diet period, whereas a single symmetrical elution peak was found for chow-fed HDL. Thus on a cholesterol-fat diet, HDL2 and HDL3 increased in difference in molecular size.     

Serum concentrations of oestradiol and progesterone during the normal oestrous cycle and early pregnancy in the lion (Panthera leo)

During a 6-month study period weekly serum samples demonstrated 9 oestradiol surges above 14 pg/ml (range 19-108 pg/ml) among 3 lionesses isolated from male lions. Intervals between peaks ranged from 3 to 8 weeks. Progesterone surges of more than 17 ng/ml (range 17-282 ng/ml) and lasting for 2-6 weeks were recorded after 7 of the oestradiol peaks. Sexual behaviour correlated well with the oestradiol peaks. Except for cornification following oestradiol peaks, there was no obvious vaginal cytology pattern at other times of the cycle. Pregnancy occurred after a 12-h contact with a male during behavioural oestrus. During gestation (108 days) oestradiol values remained low, while progesterone was elevated to 49 ng/ml within 12 h after mating, reaching a peak of 143 ng/ml at the 4th week, and remaining elevated during the next 2 months.     

The unique action for bone metabolism of 1 alpha,25-(OH)2D3-26,23-lactone

[23 (S), 25 (R)]-1 alpha,25-Dihydroxyvitamin D3-26,23-lactone [( 23 (S),25 (R)]-1 alpha,25-(OH) 2D3-26,23-lactone) increased dose-dependently alkaline phosphatase activity in osteoblastic cells, clone MC3T3-E1, in medium containing 0.1% bovine serum albumin. The maximal stimulated enzyme activity per mg protein was 1.6-fold over that of control cultures at 250 pg/ml. The metabolite also increased collagen synthesis in a dose-related fashion. On the other hand, [23 (S),25 (R)]-1 alpha,25-(OH)2D3-26,23-lactone decreased slightly but significantly 45Ca mobilization, and blocked the resorptive action of 1 alpha,25-dihydroxyvitamin D3 but not that of parathyroid hormone, in mouse calvaria in organ culture. These results indicate that [23 (S),25 (R)]-1 alpha, 25-(OH)2D3-26,23-lactone stimulates the differentiation of osteoblasts and inhibits bone resorption in vitro.     

Effect of immunoaffinity depletion of human serum during proteomic investigations

Controversy exists regarding the proper mining of the human serum proteome. Because of the analytical challenges of accurately measuring samples containing a very large dynamic range of protein concentrations, current practices have employed depletion of the highly abundant housekeeping serum proteins, such as albumin and immunoglobins. There is question as to the selectivity of depletion, namely, is there loss of other non abundant serum proteins along with albumin, haptoglobin and other commonly depleted proteins. In this study, human serum was analyzed with and without immunoaffinity depletion of the six most abundant proteins by multidimensional liquid chromatography tandem mass spectrometry. Two replicates of each experiment were conducted and compared against one another. In both depleted and nondepleted replicates there was a 73% and 72% overlap of identified peptides and a 64% and 78% overlap of identified proteins, respectively. Of 262 unique proteins identified in the four experiments, 82 were found in common to all four experiments, 142 unique to the depleted serum, and 38 unique to the nondepleted serum. Although serum depletion of highly abundant proteins significantly increased the number of proteins identified, both the degree of sample complexity and this depletion method resulted in a nonselective loss of other proteins.     

Trypanosoma equiperdum: Active immunization of rabbits with actinomycin D-inactivated parasites

Trypanosoma equiperdum was inactivated with actinomycin D. Rabbits inoculated with inactivated parasites were completely protected from a challenge inoculation of viable T. equiperdum of the same stabilate. Immune serum from the inoculated rabbits, as well as the 7 S and 19 S serum fractions, were tested for their ability to neutralize trypanosomes. During the first 6 weeks of immunization the neutralizing activity of the 19 S fraction was stronger than that of the 7 S fraction. After 9 weeks, the situation was reversed.     

Changes in soil phosphorus fractions following sole cropped and intercropped maize and faba bean grown on calcareous soil

Aims

This study aimed to investigate the effects of coexistence with faba bean, a phosphorus (P)-efficient crop, on soil-accumulated P use by a maize/faba bean intercropping system on dynamic changes in soil P pool.

Methods

Maize and faba bean were grown in P-accumulated soil as either sole cropping or intercropping. After one year (Stage I) or four years (Stage II) of no P application, soil samples were collected respectively and analyzed for soil P pools using sequential fractionation. Aboveground biomass and P content were annually measured from 2013 to 2016 to assess the annual P balance.

Results

The intercropped maize/faba bean system showed a P-uptake advantage, with a Land Equivalent Ratio (LER) ranging from 1.2 to 1.5. The average shoot P content over the four years in intercropped maize and faba bean was significantly greater than that of the corresponding sole crops by 29% and 30%, respectively. Over the three-year P depletion period, the three cropping systems primarily depleted the 1 M HCl-P_i fraction, followed by sole maize, which depleted the NaOH-P_i and concentrated HCl-P_o fractions. Sole faba bean depleted the alkali-soluble P_o fraction (extracted by NaHCO₃ and NaOH), and the intercropped maize/faba bean system depleted the conc. HCl-P_o fraction, which was similar to the effect of sole maize.

Conclusions

Both sole crops and intercrops mainly depleted 1 M HCl-P_i, but differed in P_o depletion. Sole maize and maize/faba bean intercropping depleted the sparingly labile P_o fraction, while sole faba bean depleted the labile and moderately labile P_o fractions.

     

A novel alignment method and multiple filters for exclusion of unqualified peptides to enhance label-free quantification using peptide intensity in LC-MS/MS

Though many software packages have been developed to perform label-free quantification of proteins in complex biological samples using peptide intensities generated by LC-MS/MS, two critical issues are generally ignored in this field: (i) peptides have multiple elution patterns across runs in an experiment, and (ii) many peptides cannot be used for protein quantification. To address these two key issues, we have developed a novel alignment method to enable accurate peptide peak retention time determination and multiple filters to eliminate unqualified peptides for protein quantification. Repeatability and linearity have been tested using six very different samples, i.e., standard peptides, kidney tissue lysates, HT29-MTX cell lysates, depleted human serum, human serum albumin-bound proteins, and standard proteins spiked in kidney tissue lysates. At least 90.8% of the proteins (up to 1,390) had CVs ≤ 30% across 10 technical replicates, and at least 93.6% (up to 2,013) had R(2) ≥ 0.9500 across 7 concentrations. Identical amounts of standard protein spiked in complex biological samples achieved a CV of 8.6% across eight injections of two groups. Further assessment was made by comparing mass spectrometric results to immunodetection, and consistent results were obtained. The new approach has novel and specific features enabling accurate label-free quantification.     

Progressive degradation of serum samples limits proteomic biomarker discovery

Preanalytical variables play a key role in discovery of biomarkers. Although the effect of several preanalytical variables on the mass spectral profiles has been studied extensively, little is known about long-term storage of serum samples. This is important because samples used in case-control or epidemiological studies are usually stored for a long time before analysis. Here we evaluated long-term storage effects on mass spectral peak patterns of serum peptides extracted using weak cation exchange magnetic beads. For this, 20 serum samples stored at −80 °C were divided equally into two groups based on their storage time. We found that intensities of 26 mass spectral peaks significantly varied between these two groups. Intensities of these peaks significantly correlated with storage time. Genetic algorithm-based models generated using these 26 peaks could classify 63 additional samples into these two groups with 100% and 96% accuracy, respectively. We also show that storing samples for 10 months at −80 and −20 °C results in the appearance/disappearance or intensity variation of peaks, some of which were previously reported as disease biomarkers.     

Peak quantification in surface-enhanced laser desorption/ionization by using mixture models

Surface-enhanced laser desorption/ionization (SELDI) time of flight (TOF) is a mass spectrometry technology for measuring the composition of a sampled protein mixture. A mass spectrum contains peaks corresponding to proteins in the sample. The peak areas are proportional to the measured concentrations of the corresponding proteins. Quantifying peak areas is difficult for existing methods because peak shapes are not constant across a spectrum and because peaks often overlap. We present a new method for quantifying peak areas. Our method decomposes a spectrum into peaks and a baseline using so-called statistical finite mixture models. We illustrate our method in detail on 8 samples from culture media of adipose tissue and globally on 64 samples from serum to compare our method to the standard Ciphergen method. Both methods give similar estimates for singleton peaks, but not for overlapping peaks. The Ciphergen method overestimates the heights of such peaks while our method still gives appropriate estimates. Peak quantification is an important step in pre-processing SELDI-TOF data and improvements therein will pay off in the later biomarker discovery phase.     

An alternative method for serum protein depletion/enrichment by precipitation at mildly acidic pH values and low ionic strength

Serum proteome analysis is severely hampered by the extreme dynamic range of protein concentrations, but tools for the specific depletion of highly abundant serum proteins lack for most farm and companion animals. A well‐established alternative strategy to reduce the dynamic range of plasma protein concentrations, treatment with combinatorial peptide ligand libraries (CPLL), is generally applicable but requires large amounts of sample. Therefore, additional depletion/enrichment protocols for plasma and serum samples from animals are desirable. In this respect, we have tested a protein precipitate that formed after withdrawal of salt from human, bovine, or porcine serum at pH 4.2. The bovine sample was composed of over 300 proteins making it a potential source for biomarker discovery. Precipitation was highly reproducible and the concentrations of albumin and other highly abundant serum proteins were strongly reduced. In comparison to the CPLL treatment, precipitation did not introduce any selection bias based on hydrophathy or pI. However, the composition of both preparations was partially complementary. Salt withdrawal at pH 4.2 is suggested as additional depletion/enrichment strategy for serum samples. Also, we point out that the removal of precipitates from serum samples under the described conditions bears the risk of losing a valuable protein fraction.     

XeCl准分子紫外激光辐照生物大分子BSA(V)对其蛋白质结构的影响

XeCl(308 nm)准分子紫外激光(单脉冲输出能量25 mJ,33.3 mJ~34.4 mJ,脉冲频率每秒两次,光斑15 mm×7 mm或4.5 mm×0.5 mm,透镜焦距300 mm),辐照小牛血清白蛋白[bovine serum albumin fraction V,BSA(V)]固体或溶液样品的时间分别为15 s、30 s、45 s或60 s;样品距激光光源的距离分别为:150 mm、250mm、290 mm、340 mm。改变激光参量辐照BSA(V)样品和其对照,用光谱法测试其FT-IR(IR)、Vis-UV(UV)、FR光谱,并比较分析。受辐照后的BSA(V)与主链构象相关的酰胺平面的特征FT-IR谱线,特别是与蛋白质二级结构敏感的酰胺面Ⅰ,1 652 cm-1;与α-螺旋结构相关的FT-IR 1 140 cm-1~500 cm-1;及与蛋白质侧链氨基酸残基Tyr、Phe、Trp相关的特征峰UV277.6 nm、UV216 nm和FR 340 nm、FR 680 nm的峰强度(T%或OD%或Q%)和它们的峰位(cm-1或nm)均受激光辐照的影响,其影响程度与使用的XeCl激光参量的改变有一定的敏感性和相关性。实验结果与讨论对认识激光生物学效应的分子机理、探索建立激光-生物学效应的关系参数,以便进一步发现新的有效的激光生物学效应,发现和认识潜在(后继)的正、负面的激光生物学效应,进而加以调控有一定的理论与实用参考价值。     

Identification of a plausible biosynthetic enzyme for the IM-2-type autoregulator in Streptomyces antibioticus

Virginiae butanolides (VBs) and IM-2 are members of Streptomyces hormones called 'butyrolactone autoregulators' which regulate the antibiotic production in Streptomyces species at nanomolar concentrations. Cell-free extract of a VB-A overproducer, Streptomyces antibioticus NF-18, is capable of catalyzing the final step of the autoregulator biosynthesis, namely, the NADPH-dependent reduction of 6-dehydroVB-A. However, physico-chemical analyses of the purified enzymatic products revealed that, in addition to the VB-type isomer [(2R,3R,6S)-enantiomer], IM-2-type isomers [(2R,3R, 6R)- and (2S,3S,6S)-enantiomers] were also produced from (+/-)-6-dehydroVB-A, suggesting the existence of several 6-dehydroVB-A reductases with respective stereoselectivities. The reductase activity of the crude extracts was separated into two activity peaks, peak I (major) and peak II (minor), by DEAE-5PW HPLC. Chiral HPLC analyses demonstrated that peak I enzyme and peak II enzyme catalyzed the production of (2R,3R,6S), (2R,3R,6R) and (2S,3S, 6S) isomers at ratios of 46:1:3.2 and 4.9:1:1.5, respectively, indicating clearly that S. antibioticus NF-18 possesses at least two 6-dehydroVB-A reductases: one much favored toward VB-A biosynthesis, the other with relaxed stereoselectivity capable of synthesizing both VB-type and IM-2-type autoregulators.