Comparative analysis of Erk phosphorylation suggests a mixed strategy for measuring phospho‐form distributions

The functional impact of multisite protein phosphorylation can depend on both the numbers and the positions of phosphorylated sites—the global pattern of phosphorylation or ‘phospho‐form’—giving biological systems profound capabilities for dynamic information processing. A central problem in quantitative systems biology, therefore, is to measure the ‘phospho‐form distribution’: the relative amount of each of the 2ⁿ phospho‐forms of a protein with n‐phosphorylation sites. We compared four potential methods—western blots with phospho‐specific antibodies, peptide‐based liquid chromatography (LC) and mass spectrometry (MS; pepMS), protein‐based LC/MS (proMS) and nuclear magnetic resonance spectroscopy (NMR)—on differentially phosphorylated samples of the well‐studied mitogen‐activated protein kinase Erk2, with two phosphorylation sites. The MS methods were quantitatively consistent with each other and with NMR to within 10%, but western blots, while highly sensitive, showed significant discrepancies with MS. NMR also uncovered two additional phosphorylations, for which a combination of pepMS and proMS yielded an estimate of the 16‐member phospho‐form distribution. This combined MS strategy provides an optimal mixture of accuracy and coverage for quantifying distributions, but positional isomers remain a challenging problem.     

The influence of storage on the “chemical age” of red wines

Storage conditions and duration have a considerable influence on wine quality. Optimum temperature and humidity conditions may improve wine quality through ageing, while incorrect or excessively long storage leads to negative results. In order to evaluate the global effects of storage on red wine composition, 20 Sangiovese wines were stored in two different conditions (cellar or house) for a period of 2 years and analysed every 6 months. Untargeted LC–MS analysis showed various putative markers for the type and length of conservation (i.e. pigments, flavanols, pantothenic acid etc.), while targeted LC–MS confirmed and expanded these results within specific metabolic groups. The results of multivariate analysis showed that wines stored in the cellar changed little even after 2 years of storage, while wines stored in typical domestic conditions (house) developed approximately four times faster, reaching a composition similar to wines stored in the cellar for 2 years after just 6 months. The formation of several monosulfonated flavanols during domestic ageing provided the first evidence in wine of a reaction between wine tannins—both catechins and proanthocyanidins—and the exogenous antioxidant bisulfite. Moreover, ageing in domestic conditions appeared to induce an accelerated decrease in wine pigments, while specifically promoting the formation of pinotin A-like pigments and the hydrolysis of flavonol glycosides.     

Chromatography and Characterization of Phenylglycidyl Ether Nucleoside Adducts

Abstract

The HPLC separation and structure elucidation (UV, NMR, MS) of the nucleoside adducts formed between 2′—deoxyadenosine, thymidine, 2′—deoxycytidine and 2′—deoxyguanosine with phenylglycidyl ether is described.     

Mass Spectrometry‐Based Analysis of Time‐Resolved Proteome Quantification

The aspect of time is essential in biological processes and thus it is important to be able to monitor signaling molecules through time. Proteins are key players in cellular signaling and they respond to many stimuli and change their expression in many time‐dependent processes. Mass spectrometry (MS) is an important tool for studying proteins, including their posttranslational modifications and their interaction partners—both in qualitative and quantitative ways. In order to distinguish the different trends over time, proteins, modification sites, and interacting proteins must be compared between different time points, and therefore relative quantification is preferred. In this review, the progress and challenges for MS‐based analysis of time‐resolved proteome dynamics are discussed. Further, aspects on model systems, technologies, sampling frequencies, and presentation of the dynamic data are discussed.     

Quantification of the Dynamic Phosphorylation Process of ERK Using Stable Isotope Dilution Selective Reaction Monitoring Mass Spectrometry

Mitogen‐activated protein (MAP) kinase signaling is critical for various cellular responses, including cell proliferation, differentiation, and cell death. The MAP kinase cascade is conserved in the eukaryotic kingdom as a three‐tiered kinase module—MAP kinase kinase kinase, MAP kinase kinase, and MAP kinase—that transduces signals via sequential phosphorylation upon stimulation. Dual phosphorylation of MAP kinase on the conserved threonine‐glutamic acid‐tyrosine (TEY) motif is essential for its catalytic activity and signal activation; however, the molecular mechanism by which the two residues are phosphorylated remains elusive. In the present study, the pattern of dual phosphorylation of extracellular signal‐regulated kinase (ERK) is profiled on the TEY motif using stable isotope dilution (SID)‐selective reaction monitoring (SRM) mass spectrometry (MS) to elucidate the order and magnitude of endogenous ERK phosphorylation in cellular model systems. The SID‐SRM‐MS analysis of phosphopeptides demonstrates that tyrosine phosphorylation in the TEY motif is dynamic, while threonine phosphorylation is static. Analyses of the mono‐phosphorylatable mutants ERK^T202A and ERK^Y204F indicate that phosphorylation of tyrosine is not affected by the phosphorylation state of threonine, while threonine phosphorylation depends on tyrosine phosphorylation. The data suggest that dual phosphorylation of ERK is a highly ordered and restricted mechanism determined by tyrosine phosphorylation.     

Hydroxyl and 1-hydroxyethyl free radical detection using spin traps followed by derivatization and gas chromatography—mass spectrometry

Summary

Detection of hydroxyl free radicals is frequently performed by electron spin resonance (ESR) following spin trapping of the radical using 5,5-dimethylpyrroline N-oxide (DMPO) to generate a stable free radical having a characteristic ESR spectrum. The necessary ESR equipment is expensive and not readily available to many laboratories. In the present study, a specific and sensitive gas chromatography—mass spectrometry (GC/MS) method for detection of hydroxyl and hydroxyethyl free radicals is described. The DMPO or N-t-butyl—α—phenylnitrone (PBN) radical adducts are extracted and derivatized by trimethylsylilation and analyzed by GC/MS. To standardize the method, ^.OH and 1-hydroxyethyl radicals were generated in two different systems: 1) a Fenton reaction in a pure chemical system in the absence or presence of ethanol and 2) in liver microsomal suspensions where ethanol is metabolized in the presence of NADPH. In the Fenton system both radicals were easily detected and specifically identified using DMPO or PBN. In microsomal suspensions DMPO proved better for detection of ^.OH radicals and PBN more suitable for detection of 1-hydroxyethyl radicals. The procedure is specific, sensitive and potentially as useful as ESR.     

Transformation of Brassica napus Using Agrobacterium tumefaciens and Regeneration of Transgenic Plants

Seeds of Brassica napus L. cv. "Yunbei 2" were surface-sterilized and germinated on hormone-free MS medium. After 4—5 days the cotyledons were excised in such a way that each has a 1—2 mm petiole was remained at its base. These cotyledons were used as the explants for tissue culture and genetic transformation. This paper first deals with the improvement of the medium for shoot regeneration. Of the elements tested, AgNO3 and carbenicillin enhanced shoot regeneration. The highest frequency (52 %) was obtained on MS medium containing 4.5 mg/L BAP, 20 μmol/L AgNOa and 500 mg/L earbenicillin. An efficient gene transfer system based on the regeneration procedure was established. After 2 days of cocultivation with Agrobacterium tumefaciens strain A208SE (pTi T37-SE, pROA93), the explants were transferred onto selection medium containing 25 mg/L kanamycin. After 1.5 months shoots emerged from 27% of the explants inoculated. They were excised and transferred onto rooting medium containing 25 mg/L kanamycin and 200 mg/L cefotaxime which is better than carbenicillin for root induction. Whole plants were transplanted into pots, and grew well in the phytotron. Transformation was confirmed by β-glueuronidase assay and Southern blotting analysis.     

In vitro propagation and production of cardiotonic glycosides in shoot cultures of Digitalis purpurea L. by elicitation and precursor feeding

Digitalis purpurea L. (Scrophulariaceae; Foxglove) is a source of cardiotonic glycosides such as digitoxin and digoxin which are commercially applied in the treatment to strengthen cardiac diffusion and to regulate heart rhythm. This investigation deals with in vitro propagation and elicited production of cardiotonic glycosides digitoxin and digoxin in shoot cultures of D. purpurea L. In vitro germinated seedlings were used as a primary source of explants. Multiple shoot formation was achieved for three explant types (nodal, internodal, and leaf) cultured on Murashige and Skoog (MS) medium with several treatments of cytokinins (6-benzyladenine—BA; kinetin—Kin; and thidiazuron—TDZ) and auxins (indole-3-acetic acid—IAA; α-naphthaleneacetic acid—NAA; and 2,4-dichlorophenoxy acetic acid—2,4-D). Maximum multiple shoots (12.7?±?0.6) were produced from nodal explants on MS?+?7.5 μM BA. Shoots were rooted in vitro on MS containing 15 μM IAA. Rooted plantlets were successfully acclimatized. To further maintain the multiple shoot induction, mother tissue was cut into four equal parts and repeatedly sub-cultured on fresh shoot induction liquid medium after each harvest. On adaptation of this strategy, an average of 18 shoots per explant could be produced. This strategy was applied for the production of biomass and glycosides digitoxin and digoxin in shoot cultures on MS medium supplemented with 7.5 μM BA and several treatments with plant growth regulators, incubation period, abiotic (salicylic acid, mannitol, sorbitol, PEG-6000, NaCl, and KCl), biotic (Aspergillus niger, Helminthosporium sp., Alternaria sp., chitin, and yeast extract) elicitors, and precursors (progesterone, cholesterol, and squalene). The treatment of KCl, mycelial mass of Helminthosporium sp., and progesterone were highly effective for the production of cardenolides. In the presence of progesterone (200 to 300 mg/l), digitoxin and digoxin accumulation was enhanced by 9.1- and 11.9-folds respectively.     

An efficient heuristic for scheduling batches of parts in a flexible flow system

Flexible manufacturing systems (FMSs) are a class of automated systems that can be used to improve productivity in batch manufacturing. Four stages of decision making have been defined for an FMS—the design, planning, scheduling, and control stages. This research focuses on the planning stage, and specifically in the area of scheduling batches of parts through the system. The literature to date on the FMS planning stage has mostly focused on the machine grouping, tool loading, and parttype selection problems. Our research carries the literature a step further by addressing the problem of scheduling batches of parts. Due to the use of serial-access material-handling systems in many FMSs, the batch-scheduling problem is modeled for a flexible flow system (FFS). This model explicitly accounts for setup times between batches that are dependent on their processing sequence. A heuristic procedure is developed for this batch-scheduling problem—the Maximum Savings (MS) heuristic. The MS heuristic is based upon the savings in time associated with a particular sequence and selecting the one with the maximum savings. It uses a two-phase method, with the savings being calculated in phase I, while a branch-and-bound procedure is employed to seek the best heuristic solution in phase II. Extensive computational results are provided for a wide variety of problems. The results show that the MS heuristic provides good-quality solutions.     

Exploring <Emphasis Type="Italic">in vitro</Emphasis> germplasm conservation options for sugarcane (<Emphasis Type="Italic">Saccharum</Emphasis> spp. hybrids) in South Africa

In vitro plantlets of sugarcane cultivar NCo310 were maintained in slow growth conditions at both 18 and 24°C and on four semi-solid media: SG1—Murashige and Skoog (MS) salts and vitamins with 20 g L^?1 sucrose, SG2—½ MS with 10 g L^?1 sucrose, SG3—MS with 20 g L^?1 sucrose and 1 mg L^?1 abscisic acid (ABA), and SG4—½ MS with 10 g L^?1 sucrose and 1 mg L^?1 ABA. After 8, 12, 24, 36, and 48 mo shoot multiplication rates were recorded, shoots were removed from storage and subcultured every 2 wk on SG1 with 0.015 mg L^?1 kinetin and 0.1 mg L^?1 benzyl aminopurine for 2 mo. At 18°C, all media supported storage for 48 mo with subculturing every 12 mo. Shoot multiplication post-retrieval was significantly higher on the SG2 medium compared with the non-stored control (362 ± 84 and 126 ± 26 shoots per recovered shoot after 2 mo, respectively). In addition, shoots could be maintained for 48 mo on SG2 medium with one subculture without compromising post-storage multiplication ability. At 24°C, storage on all four media supported recovery and multiplication of shoots for 8 mo and only SG2 medium facilitated survival for 12 mo. There was no advantage to incorporating ABA into the storage media, regardless of the temperature and storage time. Cryopreservation of cultivar NCo376 in vitro-derived shoot meristems using the V-cryo-plate method demonstrated that the sucrose concentration in the loading solution (0.8–1.8 M) had no significant effect on survival of the meristems, which ranged from 41.7 ± 4.8 to 69.4 ± 10%.     

Plant Regeneration from Protoplasts of Suspension Cells of Saposhnilkovia divaricata (Turcz.) Schischk

Embryogenic calli were produced from the segments of the young roots, hypocotyls or petioles of test-tube seedlings on MS agar medium containing 1 mg/1 2,4-D. When shaken in the MS liquid medium, the calli formed cell suspension with many embryogenic cell clumps.Using the enzyme mixture: Onozuka R-10 1.5%+MacerozymeR-10 0.3%+Snailase 0.5%+CaCl2 5 mmol/l + Mannitol 0.6 mol/1 (pH=5.8), protoplasts were obtained from the cell clumps which had been subcultured for three to' seven days. When cultivated, the protoplasts grew and began to divide after four days, and formed cell clumps about l—2 mm within fifty days. Protoplast-derived calli were formed from the cell clumps on the MS agar medium with 0.5 mg/l 2,4-D. When transferred onto the MS agar medium containing 0.1 mg/1 6-BA or 0.1 mg/1 2,4-D and 0.5 mg/1 6-BA, the calli differentiated into embryoids. On the MS agar medium without phytohormone, the embryoids grew into plantlets.     

Whole cell,label free protein quantitation with data independent acquisition: Quantitation at the MS2 level

Label free quantitation by measurement of peptide fragment signal intensity (MS2 quantitation) is a technique that has seen limited use due to the stochastic nature of data dependent acquisition (DDA). However, data independent acquisition has the potential to make large scale MS2 quantitation a more viable technique. In this study we used an implementation of data independent acquisition—SWATH—to perform label free protein quantitation in a model bacterium Clostridium stercorarium. Four tryptic digests analyzed by SWATH were probed by an ion library containing information on peptide mass and retention time obtained from DDA experiments. Application of this ion library to SWATH data quantified 1030 proteins with at least two peptides quantified (～40% of predicted proteins in the C. stercorarium genome) in each replicate. Quantitative results obtained were very consistent between biological replicates (R² ～ 0.960). Protein quantitation by summation of peptide fragment signal intensities was also highly consistent between biological replicates (R² ～ 0.930), indicating that this approach may have increased viability compared to recent applications in label free protein quantitation. SWATH based quantitation was able to consistently detect differences in relative protein quantity and it provided coverage for a number of proteins that were missed in some samples by DDA analysis.     

板栗疫病菌致病性机理的双向凝胶电泳法研究

双向凝胶电泳技术是蛋白质组学研究的基础性技术平台。如何得到一张高质量的双向凝胶电泳图谱是进行后续研究的关键。为探索适用于板栗疫病菌可溶性总蛋白的最佳提取条件,从蛋白组学角度来探索板栗疫病菌致病性机理,比较了目前在丝状真菌中常用的两种蛋白质提取方法,制备的蛋白质样品经双向凝胶电泳后,在凝胶上呈现的蛋白质斑点的丰度和分布特点。结果表明,两种方法获得的蛋白质主要集中分布在pH4~7的范围内;TCA-丙酮沉淀法得到的图谱分辨率高但是蛋白质总量很少。裂解液-TCA-丙酮沉淀法得到的蛋白质总量较大,通过cleanupkit处理后图谱分辨率可以达到差异蛋白组的要求。随机提取几个银染蛋白点用MALDI-TOFMS/MS进行分析,可以得到高质量的肽质量指纹谱。表明该样品制备方法可以满足蛋白质鉴定的要求。     

In Vitro Culture and Regeneration of Solanum khasianum and Extraction of Solasodine

Leaf explants of Solanum khasianum regenerated on MS medium containing 2, 4-D (3 mg/l) and kinetin (1 mg/l). Shoots could be induced from these calli on medium containing BAP (3 mg/l) alone. Rhizogenesis of these shoots occurred when transferred to medium containing 2 mg/l NAA. The yield of solasodine — a pharmaceutically important compound, from 4-month-old callus tissue was remarkable at 2 per cent of dry weight.     

Improved two-dimensional reversed phase-reversed phase LC-MS/MS approach for identification of peptide-protein interactions

Quantitative mass spectrometry (MS) in combination with affinity purification approaches allows for an unbiased study of protein-protein and peptide-protein interactions. In shotgun approaches that are based on proteolytic digestion of complex protein mixtures followed by two-dimensional liquid-phase chromatography, the separation effort prior to MS analysis is focused on tryptic peptides. Here we developed an improved offline 2-D liquid chromatography-MS/MS approach for the identification and quantification of binding proteins utilizing reversed-phase capillary columns with acidic acetonitrile-containing eluents in both chromatographic dimensions. A specific fractionation scheme was applied in order to obtain samples with evenly distributed peptides and to fully utilize the separation space in the second dimension nanoLC-MS/MS. We report peptide-protein interaction studies to identify phosphorylation-dependent binding partners of the T cell adapter protein ADAP. The results of the SILAC-based pull-down experiments show this approach is well suited for distinguishing phosphorylation-specific interactions from unspecific binding events. The data provide further evidence that phosphorylated Tyr 595 of ADAP may serve as a direct binding site for the SH2 domains of the T cell proteins SLP76 and NCK. From a technical point of view we provide a detailed protocol for an offline 2-D RP-RP LC-MS/MS method that offers a robust and time-saving alternative for quantitative interactome analysis.     

Immunolocalization of glyoxysomal malate synthase from soybean cotyledons (Glycine max L)

Summary— Malate synthase (MS; EC 4.1.3.2), an enzyme specific to the glyoxylate cycle, was studied in cotyledons of dark-grown soybean (Glycine max L) seedlings with light and electron microscopy techniques. Immunogold localization confirmed biochemical evidence that MS from soybean is a glyoxysomal matrix enzyme.     

Proteomics of CaCO3 biomineral‐associated proteins: How to properly address their analysis

In a recent editorial (Proc. Natl. Acad. Sci., 2013 110, E2144–E2146) and elsewhere, questions have been raised regarding the experimental practices in relation to the proteomic analysis of organic matrices associated to the biomineralized CaCO₃ skeletons of metazoans such as molluscan shells and coral skeletons. Indeed, although the use of new high sensitivity MS technology potentially allows to identify a greater number of proteins, it is also equally (or even more) sensitive to contamination of residual proteins from soft tissues, which are in close contact with the biomineral. Based on our own past and present experimental know‐how—observations that are reproducible and coherent with the current understanding of extracellular biomineralization processes—we are convinced that a careful and appropriate cleaning of biominerals prior to any analysis is crucial for accurate proteomic investigations and subsequent pertinent interpretation of the results. Our goal is to alert the scientific community about the associated bias that definitely should be avoided, and to provide critical recommendations on sample preparation and experimental design, in order to better take advantage of the aptness of proteomic approaches aiming at improving our understanding of the molecular mechanisms in biomineralization.     

Microbicidal and anti-inflammatory effects of Actinomadura spadix (EHA-2) active metabolites from Himalayan soils, India

Actinomycetes play an essential role in producing several bioactive compounds. In the present study, microbicidal and anti-inflammatory effects of metabolites from actinomycetes were investigated. Actinomycetes were isolated from north eastern Himalayan soil samples, India. The actinomycetes were investigated for their microbicidal property by conventional method and the active actinomycetes were identified by 16s rDNA sequence analyses. Further the metabolites were extracted and fractionated to evaluate the antimicrobial potency; they were subjected to GC–MS analysis. The active fraction was evaluated for selective toxicity and anti-inflammatory potential. Among isolated actinomycetes, EHA-2 showed potent antimicrobial activity and was identified as Actinomadura spadix. Fraction-8 from ethyl acetate extract of EHA-2 showed 100 % inhibition against Candida sp. (MIC—80 μg/mL) and Enterococcus faecalis (MIC—80 μg/mL). The expression of GAPDH in primary cells and 16s rRNA levels on E. faecalis treated with fraction-8 revealed no toxicity to the primary cells. Fraction-8 also suppressed the paw thickness on carrageenan induced animals and also controlled the release of NO, TNFα and IL-1β levels on LPS induced RAW 264.7 cell lines. GC–MS profile of fraction-8 showed the presence of an antimicrobial agent 3,6 di-isobutyl 2,5 piperazinedione, which is the first report in A. spadix. The actinomycetes isolate EHA-2 can be proceed further to produce antibiotics.     

Effect of the sequences upstream from the ribosome-binding site on the yield of protein from the cloned gene for phage MS2 coat protein

The translational efficiency of the coat protein gene of phage MS2 has been examined in vivo with respect to neighbouring sequences. The cloned MS2 DNA has been gradually shortened starting at the 5' or 3' terminus, and its effect on coat protein synthesis monitored. Removal of the 3'-terminal sequences had little influence. In contrast, the gradual removal of the 5'-terminal region profoundly reduces translation. Long before the ribosomal binding site (RBS) of the coat protein (CP) gene is reached, the yield of CP has dropped by one order of magnitude. Functional half-lives of the various messengers were found not to be significantly different. Available evidence indicates that the secondary structure of the RBS in native and shortened MS2 RNA is identical. We infer that important determinants for ribosome recognition lie 5' to the RBS region of the MS2 RNA coat gene.