Effect of CyDye minimum labeling in differential gel electrophoresis on the reliability of protein identification

Differential 2-DE (DIGE) is a widely applied tool for the quantitative analysis of differentially represented proteins. The method involves covalent minimal labeling of proteins prior to their electrophoretic separation using CyDye DIGE Fluor minimal dyes. This methodology creates two different species per protein, the labeled (approx. 1-2%) and unlabeled (approx. 98-99%) ones, which differ in their molecular masses by 434-464 Da, depending on the attached dye. DIGE followed by automated spot picking according to the CyDye coordinates misses in many instances the exact positions where the maximum amounts of the considered proteins are located. This fact leads to a loss in sensitivity of the subsequent MALDI-MS analyses and results in a reduced reliability of protein identification and sequence coverage. In this paper, the migration differences of labeled and unlabeled species are quantified together with the impact of this effect on the certainty of protein identification and sequence coverage investigating proteins up to 90 kDa.     

Synthesis and characterization of the open-framework barium bisphosphonate [Ba3(O3PCH2NH2CH2PO3)2(H2O)4].3H2O

Following the strategy of using polyfunctional phosphonic acids for the synthesis of open-framework metal phosphonates, the phosphonocarboxylic acid (H2O3PCH2)2NCH2C6H4COOH was used in the hydrothermal synthesis of new Ba phosphonates. Its decomposition led to the first open-framework barium phosphonate [Ba3(O3PCH2NH2CH2PO3)2(H2O)4].3H2O. The synthesis was also successfully performed using iminobis(methylphosphonic acid), (H2O3PCH2)2NH, as a starting material, and the synthesis was optimized to obtain as a pure material. The reaction setup as well as the pH are the dominant parameters, and only a diffusion-controlled reaction led to the desired compound. The crystal structure was solved from single-crystal data: monoclinic; C2/c; a=2328.7(2), b=1359.95(7), and c=718.62(6) pm; beta=98.732(10) degrees ; V=2249.5(3)x10(6) pm3; Z=4; R1=0.036; and wR2=0.072 (all data). The structure of [Ba3(O3PCH2NH2CH2PO3)2(H2O)4].3H2O is built up from BaO8 and BaO10 polyhedra forming BaO chains and layers, respectively. These are connected to a three-dimensional metal-oxygen-metal framework with the iminobis(methylphosphonic acid) formally coating the inner walls of the pores. The one-dimensional pores (3.6x4 A) are filled with H2O molecules that can be thermally removed. Thermogravimetric investigations and temperature-dependent X-ray powder diffraction demonstrate the stability of the crystal structure up to 240 degrees C. The uptake of N,N-dimethylformamide and H2O by dehydrated samples is demonstrated. Furthermore, IR, Raman, and 31P magic-angle-spinning NMR data are also presented.     

Amorphous Silicon: New Insights into an Old Material

Amorphous silicon is synthesized by treating the tetrahalosilanes SiX₄ (X=Cl, F) with molten sodium in high boiling polar and non‐polar solvents such as diglyme or nonane to give a brown or a black solid showing different reactivities towards suitable reagents. With regards to their technical relevance, their stability towards oxygen, air, moisture, chlorine‐containing reaction partners RCl (R=H, Cl, Me) and alcohols is investigated. In particular, reactions with methanol are a versatile tool to deliver important products. Besides tetramethoxysilane formation, methanolysis of silicon releases hydrogen gas under ambient conditions and is thus suitable for a decentralized hydrogen production; competitive insertion into the MeO?H versus the Me?OH bond either yields H‐ and/or methyl‐substituted methoxy functional silanes. Moreover, compounds, such as Me_nSi(OMe)_4?n (n=0–3) are simply accessible in more than 75 % yield from thermolysis of, for example, tetramethoxysilane over molten sodium. Based on our systematic investigations we identified reaction conditions to produce the methoxysilanes Me_nSi(OMe)_4?n in excellent (n=0:100 %) to acceptable yields (n=1:51 %; n=2:27 %); the yield of HSi(OMe)₃ is about 85 %. Thus, the methoxysilanes formed might possibly open the door for future routes to silicon‐based products.     

Two 2,6‐Dioxabicyclo[3.3.1]nonan‐3‐ones from Phragmanthera capitata (Spreng.) Balle (Loranthaceae)

Phytochemical investigation of the leaves of Phragmanthera capitata collected on Cassia spectabilis tree led to the isolation of two natural lactones, rel‐(1R,5S,7S)‐7‐[2‐(4‐hydroxyphenyl)ethyl]‐2,6‐dioxabicyclo[3.3.1]nonan‐3‐one ( 1 ) and 4‐{2‐[rel‐(1R,3R,5S)‐7‐oxo‐2,6‐dioxabicyclo[3.3.1]non‐3‐yl]ethyl}phenyl 3,4,5‐trihydroxybenzoate ( 2 ) together with the known compounds betulinic acid ( 3 ), dodoneine ( 4 ), quercetin 3‐O‐α‐L ‐rhamnopyranoside ( 5 ), quercetin 3‐O‐α‐L ‐arabinofuranoside ( 6 ), quercetin ( 7 ), betulin ( 8 ), lupeol ( 9 ), and sitosterol ( 10 ). Their structures were established by means of modern spectroscopic techniques, and the relative configuration of compound 1 was confirmed by X‐ray analysis. Compounds 1 and 2 were tested in vitro for their antiplasmodial activity against the Plasmodium falciparum chloroquine sensitive‐strains NF54 and 3D7. Compound 2 exhibited good antiplasmodial activity against both strains with IC₅₀ of 2.4 and 4.9 μM , respectively, while compound 1 was inactive.     

Determination of 90Sr and 210Pb in deer bone samples by liquid scintillation counting after ion-exchange procedures

This work describes a procedure for the isolation of ⁹⁰Sr and ²¹⁰Pb from deer bones by anion exchange methods and their sequential measurement by LSC. To prevent collection of Pb on the Sr·Spec^® resin we first separated Pb on a Dowex anion exchange column. Sr, which is not held back on the Dowex column, was then purified using Sr·Spec^® resin: first Ca and the Ra isotopes were eluted with 3 M HNO₃ and then Sr was eluted with distilled water. With this 2-steps procedure pure ²¹⁰Pb and ⁹⁰Sr spectra can be achieved. The chemical yield of both steps was determined by ICP-MS. Our ⁹⁰Sr results show satisfying agreement with data obtained by a shorter Sr·Spec^® method and also by the “classical” ⁹⁰Sr determination using fuming nitric acid. Also ²¹⁰Pb results were checked by re-measuring bone samples with already known ²¹⁰Pb activities. Further our method was verified on the reference sample IAEA-A-12.     

Utilization of α-olefins obtained by pyrolysis of waste high density polyethylene to synthesize α-olefin-succinic-anhydride based cold flow improvers

A new route of utilization of α-olefin rich hydrocarbon fractions obtained by waste polymer pyrolysis was investigated. α-olefin-succinic-anhydride intermediate-based pour point depressant additives for diesel fuel were synthesized, in which reactions needed α-olefins were obtained by pyrolysis of waste high-density polyethylene (HDPE). Fraction of α-olefins was produced by the de-polymerization of plastic waste in a tube reactor at 500℃ in the absence of catalysts and air. C_17~22 range of mixtures of olefins and paraffins were separated for synthesis and then, these hydrocarbons were reacted with maleic-anhydride (MA) for formation of α-olefin-succinic-anhydride intermediates. The olefin-rich hydrocarbon fraction contained approximately 60% of olefins, including 90%~95% α-olefins. Other intermediates were produced in the same way by using commercial C₂₀ α-olefin instead of C_17~22 olefin mixture. The two different experimental intermediates with number average molecular weights of 1850g/mol and 1760g/mol were reacted with different alcohols: 1-butanol, 1-hexanol, 1-octanol, i-butanol, and c-hexanol to produce their ester derivatives. The synthesized ten experimental pour point depressants were added in different concentrations to conventional diesel fuel, which had no other additive content before. The structure and efficiency of experimental additives were followed by different standardized and non-standardized methods. Results showed that the experimental additives on the basis of the product of waste pyrolysis were able to decrease not only the pour but also the cloud point and cold filter plugging point (CFPP) of diesel fuel, whose effects could be observed even if the concentration of additives was low. Furthermore, all additives had anti-wear and anti-friction effects in diesel fuel.     

New and highly efficient synthesis of 3-substituted 1-hydroxybenz[g]isoquinoline-5,10-diones

A new and efficient strategy for the synthesis of 3-substituted 1-hydroxybenz[g]isoquinoline-5,10-diones by reaction of 2-methoxycarbonyl-1,4-naphthoquinone with different pyridinium salts under Kröhnke conditions is disclosed. This one-step reaction was found to be dependent on the substitution pattern of the aromatic nucleus in the pyridinium salts.     

Synthesis and properties of allenic natural products and pharmaceuticals

Nowadays, about 150 natural products comprising an allenic or cumulenic structure are known. The chemistry of these compounds has turned out to be a very attractive and prolific area of interest: advances in the isolation and characterization of new allenic natural products have led to the establishment of efficient synthetic procedures which in many cases also open up an access to enantiomerically pure target molecules. Inspired by the intriguing biological activities of many allenic natural products, allene moieties are now systematically introduced in pharmacologically active classes of compounds (steroids, prostaglandins, amino acids, nucleosides). The functionalized allenes thus obtained often exhibit impressive activities as mechanism-based enzyme inhibitors, cytotoxic, or antiviral agents. A prerequisite for further developments in this field is the efficient stereoselective synthesis of allene derivatives.     

Fast quality assessment of German chamomile (Matricaria chamomilla L.) by headspace solid-phase microextraction: influence of flower development stage

For an adequate quality evaluation of aromatic plants grown under different conditions, a rapid, simple and sensitive method for the analysis of volatile constituents is indispensable. The main objective of the present study was to compare fast screening of German chamomile (Matricaria chamomilla L.) by means of headspace solid-phase microextraction (HS-SPME) with conventional isolation of the essential oil (steam distillation-solvent extraction (SDSE)) for the differentiation of chamomile essential oil constituents. Flowers were harvested at two distinct development stages: stage I, when ligulate flowers start to develop and tubular flowers are still closed, and stage II, when tubular flowers are partially to completely opened. Dried chamomile flowers at two development stages were extracted by means of both SDSE and HS-SPME, followed by GC-MS analysis. Among 30 compounds detected, (E)-beta-farnesene (49%), artemisia ketone (10%) and germacrene D (9%) were the predominant volatile components in the HS-SPME-extract, while alpha-bisabolol oxide A (42%), chamazulene (21%) and (Z)-spiroether (8%) were the main essential oil constituents among the 13 compounds obtained by SDSE. After statistical analysis of the data, both techniques enabled the same conclusion: (E)-beta-farnesene was the only compound which showed significant differences between the two flower development stages. These results suggest that HS-SPME-GC-MS can be used as a sensitive technique for the rapid screening and quality assessment of M. chamomilla.     

Two-dimensional electrophoresis of membrane proteins

One third of all genes of various organisms encode membrane proteins, emphasizing their crucial cellular role. However, due to their high hydrophobicity, membrane proteins demonstrate low solubility and a high tendency for aggregation. Indeed, conventional two-dimensional gel electrophoresis (2-DE), a powerful electrophoretic method for the separation of complex protein samples that applies isoelectric focusing (IEF) in the first dimension and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) in the second dimension, has a strong bias against membrane proteins. This review describes two-dimensional electrophoretic techniques that can be used to separate membrane proteins. Alternative methods for performing conventional 2-DE are highlighted; these involve replacing the IEF with electrophoresis using cationic detergents, namely 16-benzyldimethyl-n-hexadecylammonium chloride (16-BAC) and cetyl trimethyl ammonium bromide (CTAB), or the anionic detergent SDS. Finally, the separation of native membrane protein complexes through the application of blue and clear native gel electrophoresis (BN/CN-PAGE) is reviewed, as well as the free-flow electrophoresis (FFE) of membranes.