Two-stage Off-Gel isoelectric focusing: protein followed by peptide fractionation and application to proteome analysis of human plasma

This paper presents the recently introduced Off-Gel electrophoresis (OGE) technology as a versatile tool to reproducibly fractionate intact proteins and peptides into discrete liquid fractions. The coupling of two stages of OGE, i.e., the separation of intact proteins in a first-stage followed by fractionation of peptides derived from each protein fraction after proteolysis in a second stage, results in an array of 15 x 15 fractions that are directly amenable to additional peptide fractionation like reverse-phase liquid chromatography (RPC). The analysis of all second-stage peptide fractions from only the first-stage protein fraction representing pH 5.0 -5.15 by on-line reverse-phase LC-tandem mass spectrometry resulted in the identification of 53 proteins (337 peptides), of which 10 were on different immunoglobulin (Ig) chains, with an input of only 1.5 mg human blood plasma proteins. Increasing the protein load to approximately 12 mg increased the number of identified proteins in the same protein fraction to 73 proteins (449 peptides), of which 15 were Ig-related. Immunodepletion of six of the most abundant proteins (albumin, transferrin, haptoglobin, IgG, IgA, and alpha-1-antitrypsin) prior to first-stage OGE with an input of 1.5 mg of protein (equivalent to approximately 10 mg nondepleted plasma) resulted in the identification of 81 proteins (660 peptides), of which three were still Ig fragments. The pI-based separation of peptides appears to be nonuniform based on the theoretically determined pI values of identified peptides. This observation specifically accounts for the neutral zone (pI 5-8) and can be accounted for by the physicochemical properties of the peptides given by their amino acid composition. The power of OGE separation of proteins and peptides is discussed with a focus on the use of the knowledge about the pI of proteins and peptides that assist the validation of correct identifications together with the retention time of peptides on RPC.     

Versatile palladium(II)-catalyzed Negishi coupling reactions with functionalized conjugated alkenyl chlorides

Under palladium catalysis, we found that organozincate reagents, generated in situ, by reaction of Grignard compounds with less than molar amounts of zinc chloride, in the presence of conjugated alkenyl chlorides, give rapidly and cleanly the corresponding coupling product in high yields. In this way, aryl as well as primary and secondary alkyl substituents have been introduced successfully. The selectivity of the reaction allows to prepare various functionalized conjugated enynes and dienes from chloroenyne and chlorodiene derivatives bearing a functional group.     

LC-MS/MS Analysis and Comparison of Oxidative Damages on Peptides Induced by Pathogen Reduction Technologies for Platelets

Pathogen reduction technologies (PRT) are photochemical processes that use a combination of photosensitizers and UV-light to inactivate pathogens in platelet concentrates (PCs), a blood-derived product used to prevent hemorrhage. However, different studies have questioned the impact of PRT on platelet function and transfusion efficacy, and several proteomic analyses revealed possible oxidative damages to proteins. The present work focused on the oxidative damages produced by the two main PRT on peptides. Model peptides containing residues prone to oxidation (tyrosine, histidine, tryptophane, and cysteine) were irradiated with a combination of amotosalen/UVA (Intercept process) or riboflavin/UVB (Mirasol-like process). Modifications were identified and quantified by liquid chromatography coupled to tandem mass spectrometry. Cysteine-containing peptides formed disulfide bridges (R-SS-R, ?2 Da; favored following amotosalen/UVA), sulfenic and sulfonic acids (R-SOH, +16 Da, R-SO₃H, +48 Da, favored following riboflavin/UVB) upon treatment and the other amino acids exhibited different oxidations revealed by mass shifts from +4 to +34 Da involving different mechanisms; no photoadducts were detected. These amino acids were not equally affected by the PRT and the combination riboflavin/UVB generated more oxidation than amotosalen/UVA. This work identifies the different types and sites of peptide oxidations under the photochemical treatments and demonstrates that the two PRT may behave differently. The potential impact on proteins and platelet functions may thus be PRT-dependent.

Complexity of the Delaunay Triangulation of Points on Polyhedral Surfaces

It is well known that the complexity of the Delaunay triangulation of $n$ points in $\RR ^d$, i.e., the number of its simplices, can be $\Omega (n^{\lceil {d}/{2}\rceil })$. In particular, in $\RR ^3$, the number of tetrahedra can be quadratic. Put another way, if the points are uniformly distributed in a cube or a ball, the expected complexity of the Delaunay triangulation is only linear. The case of points distributed on a surface is of great practical importance in reverse engineering since most surface reconstruction algorithms first construct the Delaunay triangulation of a set of points measured on a surface. In this paper we bound the complexity of the Delaunay triangulation of points distributed on the boundary of a given polyhedron. Under a mild uniform sampling condition, we provide deterministic asymptotic bounds on the complexity of the three-dimensional Delaunay triangulation of the points when the sampling density increases. More precisely, we show that the complexity is $O(n^{1.8})$ for general polyhedral surfaces and $O(n\sqrt{n})$ for convex polyhedral surfaces. Our proof uses a geometric result of independent interest that states that the medial axis of a surface is well approximated by a subset of the Voronoi vertices of the sample points.     

Characterization of tetra,dodeca and tetradeca MoV polyoxometalate wheels structured by etidronate ligands

The reactivity of the [Mo^V₂O₄]²⁺ dinuclear unit with the [O₃P(C(CH₃)(OH))PO₃]^4? etidronate ligand has been investigated. Three complexes have been isolated and characterized by IR spectroscopy, elemental analysis and single crystal X-Ray diffraction studies. Structural determination of the tetranuclear compound (CN₃H₆)₆[(Mo^V₂O₄)₂(O₃P(C(CH₃)O)PO₃)₂]·12H₂O (1) revealed that the hydroxo group of the etidronate ligand can be deprotonated in presence of Mo^V even in acidic media. It follows that its coordination mode thus differs from that of the methylenediphosphonate ligand [O₃P(CH₂)PO3]4?, which reactivity with Mo^V has been previously widely studied. In contrast, no such deprotonation of the hydroxo group is observed in the (NH₄)₁₈[(Mo^V₂O₄)₆(OH)₆(O₃P(C(CH₃)(OH))PO₃)₆]·35H₂O complex 2. This species contains a dodecanuclear core analogous to the one previously found in the [(Mo^V₂O₄)₆(OH)₆(O₃PCH₂PO₃)₆]^18? methylenediphosphonato polyanion. In 2, six interconnected {(Mo^V₂O₄)(O₃P(C(CH₃)(OH))PO₃)} units form a cyclohexane-like ring in a chair conformation. In the (CN₃H₆)₁₈Na₃[(Mo^V₂O₄)₇(O₃P(C(CH₃)(OH))PO₃)₇(CH₃COO)₇]·5CH₃COONa 52H₂O compound 3, seven {(Mo^V₂O₄)(O₃P(C(CH₃)(OH))PO₃)(CH₃COO)} units are connected, forming an almost planar tetradecanuclear wheel. This compound represents the largest homometallic Mo^V polyoxometalate cyclic system reported to date. Finally, ³¹P NMR studies revealed that only complex 1 is stable in aqueous solution.     

Triangulations in CGAL

This paper presents the main algorithmic and design choices that have been made to implement triangulations in the computational geometry algorithms library .     

A general copper powder-catalyzed Ullmann-type reaction of 3-halo-4(1H)-quinolones with various nitrogen-containing nucleophiles

3-(N-Substituted) 4(1H)-quinolinones were synthesized using the copper-catalyzed Ullmann C-N bond forming strategy in moderate to quantitative yields. Starting from 3-halo-4(1H)-quinolones, various nucleophiles including amides, lactams, sulfonamides and NH-containing azoles have been used successfully. In all cases, the reactions take place rapidly in toluene and proceed by using copper powder as a catalyst, DMEDA as a ligand and K(2)CO(3) as a base. In addition, other related heterocycles such as 3-bromoquinolin-2(1H)-ones, 3-bromocoumarin, and 3,5-dibromo-2-pyridone show good to very high reactivity with various nucleophiles under our Cu/DMEDA catalyst system.     

Isotopic Implicit Surface Meshing

This paper addresses the problem of piecewise linear approximation of implicit surfaces. We first give a criterion ensuring that the zero-set of a smooth function and the one of a piecewise linear approximation of it are isotopic. Then, we deduce from this criterion an implicit surface meshing algorithm certifying that the output mesh is isotopic to the actual implicit surface. This is the first algorithm achieving this goal in a provably correct way.     

Water substitution on iron centers: from 0D to 1D sandwich type polyoxotungstates

Four novel polyoxotungstates have been synthesized by reaction of the sandwich type compound [Fe (III) 4(H 2O) 10(B-beta-SbW 9O 33) 2] (6-) (noted Fe 4(H 2O) 10Sb 2W 18) with ethylenediamine (en) and/or oxalate (ox) ligands under various conditions. The one-dimensional (1D) compound [enH 2] 3[Fe (III) 4(H 2O) 8(SbW 9O 33) 2].20H 2O ( 1) is isolated at 130 degrees C and results from the elimination of two water molecules and the condensation of the polyoxotungstate precursor. The reaction of Fe 4(H 2O) 10Sb 2W 18 with oxalate ligands affords the molecular complex Na 14[Fe (III) 4(ox) 4(H 2O) 2(SbW 9O 33) 2].60H 2O ( 2) where two organic ligands substitute four water molecules, while the same reaction in the presence of en molecules at 130 degrees C leads to the formation of the functionalized 1D chain [enH 2] 7[Fe (III) 4(ox) 4(SbW 9O 33) 2].14H 2O ( 3) with protonated ethylenediamine counterions. Finally, at 160 degrees C a rearrangement of the Fe 4(H 2O) 10Sb 2W 18 polyoxotungstate is observed, and the sandwich type compound [enH 2] 5[Fe (II) 2Fe (II) 2(enH) 2(Fe (III)W 9O 34) 2].24H 2O ( 4) crystallizes. In 4, the heteroelement is a Fe (III) ion, and the water molecules on the two outer Fe (II) centers are bound to pendant monoprotonated en ligands. The four compounds have been characterized by IR spectroscopy, thermogravimetric analysis, and single crystal X-ray diffraction. A detailed study of the magnetic properties of the mixed-valent hexanuclear iron complex in 4 shows evidence of an S = 5 ground-state because of spin frustration effects. A quantification of the electronic parameters characterizing the ground state ( D = +1.12 cm (-1), E/ D = 0.15) confirms that polyoxotungstate ligands induce large magnetic anisotropy.