Comparison of three methods for fractionation and enrichment of low molecular weight proteins for SELDI-TOF-MS differential analysis

In most diseases, the clinical need for serum/plasma markers has never been so crucial, not only for diagnosis, but also for the selection of the most efficient therapies, as well as exclusion of ineffective or toxic treatment. Due to the high sample complexity, prefractionation is essential for exploring the deep proteome and finding specific markers.In this study, three different sample preparation methods (i.e., highly abundant protein precipitation, restricted access materials (RAM) combined with IMAC chromatography and peptide ligand affinity beads) were investigated in order to select the best fractionation step for further differential proteomic experiments focusing on the LMW proteome (MW inferior to 40,000 Da). Indeed, the aim was not to cover the entire plasma/serum proteome, but to enrich potentially interesting tissue leakage proteins. These three methods were evaluated on their reproducibility, on the SELDI-TOF-MS peptide/protein peaks generated after fractionation and on the information supplied.The studied methods appeared to give complementary information and presented good reproducibility (below 20%). Peptide ligand affinity beads were found to provide efficient depletion of HMW proteins and peak enrichment in protein/peptide profiles.     

Rapid automated high performance liquid chromatography method for simultaneous determination of amino acids and biogenic amines in wine, fruit and honey

This paper reports a new, simple, rapid and economical method for routine determination of 24 amino acids and biogenic amines in grapes and wine. No sample clean-up is required and total run time including column re-equilibration is less than 40min. Following automated in-loop automated pre-column derivatisation with an o-phthaldialdehyde, N-acetyl-l-cysteine reagent, compounds were separated on a 3mm×25cm C(18) column using a binary mobile phase. The method was validated in the range 0.25-10mg/l; repeatability was less than 3% RSD and the intermediate precision ranged from 2 to 7% RSD. The method was shown to be linear by the 'lack of fit' test and the accuracy was between 97 and 101%. The LLOQ varied between 10μg/l for aspartic and glutamic acids, ethanolamine and GABA, and 100μg/l for tyrosine, phenylalanine, putrescine and cadaverine. The method was applied to grapes, white wine, red wine, honey and three species of physalis fruit. Grapes and physalis fruit were crushed, sieved, centrifuged and diluted 1/20 and 1/100, respectively, for analysis; wines and honeys were simply diluted 10-fold. It was shown using this method that the amino acid content of grapes was strongly correlated with berry volume, moderately correlated with sugar concentration and inversely correlated with total acidity.     

A stochastic evolution model for residue Insertion-Deletion Independent from Substitution

We develop here a new class of stochastic models of gene evolution based on residue Insertion-Deletion Independent from Substitution (IDIS). Indeed, in contrast to all existing evolution models, insertions and deletions are modeled here by a concept in population dynamics. Therefore, they are not only independent from each other, but also independent from the substitution process. After a separate stochastic analysis of the substitution and the insertion-deletion processes, we obtain a matrix differential equation combining these two processes defining the IDIS model. By deriving a general solution, we give an analytical expression of the residue occurrence probability at evolution time t as a function of a substitution rate matrix, an insertion rate vector, a deletion rate and an initial residue probability vector. Various mathematical properties of the IDIS model in relation with time t are derived: time scale, time step, time inversion and sequence length. Particular expressions of the nucleotide occurrence probability at time t are given for classical substitution rate matrices in various biological contexts: equal insertion rate, insertion-deletion only and substitution only. All these expressions can be directly used for biological evolutionary applications. The IDIS model shows a strongly different stochastic behavior from the classical substitution only model when compared on a gene dataset. Indeed, by considering three processes of residue insertion, deletion and substitution independently from each other, it allows a more realistic representation of gene evolution and opens new directions and applications in this research field.     

Vibrational spectroscopy differentiates between multipotent and pluripotent stem cells

Over the last few years, there has been an increased interest in the study of stem cells in biomedicine for therapeutic use and as a source for healing diseased or injured organs/tissues. More recently, vibrational spectroscopy has been applied to study stem cell differentiation. In this study, we have used both synchrotron based FTIR and Raman microspectroscopies to assess possible differences between human pluripotent (embryonic) and multipotent (adult mesenchymal) stem cells, and how O(2) concentration in cell culture could affect the spectral signatures of these cells. Our work shows that infrared spectroscopy of embryonic (pluripotent) and adult mesenchymal (multipotent) stem cells have different spectral signatures based on the amount of lipids in their cytoplasm (confirmed with cytological staining). Furthermore, O(2) concentration in cell culture causes changes in both the FTIR and Raman spectra of embryonic stem cells. These results show that embryonic stem cells might be more sensitive to O(2) concentration when compared to mesenchymal stem cells. While vibrational spectroscopy could therefore be of potential use in identifying different populations of stem cells further work is required to better understand these differences.     

Europium(II) compounds: simple synthesis of a molecular complex in water and coordination polymers with 2,2'-bipyrimidine-mediated ferromagnetic interactions

Reaction between EuCl(2) and 2,2'-bipyrimidine (bpm) in de-oxygenated water afforded a cationic molecular complex [EuCl(bpm)(2)(H(2)O)(4)][Cl]·H(2)O (1). When performed in an organic solvent such as THF or methanol, the same reaction yielded a 3-dimensional coordination polymer of formula [EuCl(2)(bpm)(MeOH)(0.5)](∞) (2) in which both bpm and the chloride ions act as linkers between the Eu(II) ions. Upon replacing Cl(-) by I(-), two coordination polymers of formula {[Eu(bpm)(2)(H(2)O)(3)][I](2)·0.5bpm}(∞) (3) and {[Eu(I)(bpm)(MeOH)][I]}(∞) (4) were obtained from reaction in water and methanol, respectively. All these compounds were characterized by X-ray crystallography. Investigations of the magnetic properties revealed a weak antiferromagnetic coupling in 2, while 3 and 4 showed a weak ferromagnetic coupling at low temperature.     

Submillimeter-wave and far-infrared spectroscopy of high-J transitions of the ground and ν2 = 1 states of ammonia

Complete and reliable knowledge of the ammonia spectrum is needed to enable the analysis and interpretation of astrophysical and planetary observations. Ammonia has been observed in the interstellar medium up to J=18 and more highly excited transitions are expected to appear in hot exoplanets and brown dwarfs. As a result, there is considerable interest in observing and assigning the high J (rovibrational) spectrum. In this work, numerous spectroscopic techniques were employed to study its high J transitions in the ground and ν(2)=1 states. Measurements were carried out using a frequency multiplied submillimeter spectrometer at Jet Propulsion Laboratory (JPL), a tunable far-infrared spectrometer at University of Toyama, and a high-resolution Bruker IFS 125 Fourier transform spectrometer (FTS) at Synchrotron SOLEIL. Highly excited ammonia was created with a radiofrequency discharge and a dc discharge, which allowed assignments of transitions with J up to 35. One hundred and seventy seven ground state and ν(2)=1 inversion transitions were observed with microwave accuracy in the 0.3-4.7 THz region. Of these, 125 were observed for the first time, including 26 ΔK=3 transitions. Over 2000 far-infrared transitions were assigned to the ground state and ν(2)=1 inversion bands as well as the ν(2) fundamental band. Of these, 1912 were assigned using the FTS data for the first time, including 222 ΔK=3 transitions. The accuracy of these measurements has been estimated to be 0.0003-0.0006?cm(-1). A reduced root mean square error of 0.9 was obtained for a global fit of the ground and ν(2)=1 states, which includes the lines assigned in this work and all previously available microwave, terahertz, far-infrared, and mid-infrared data. The new measurements and predictions reported here will support the analyses of astronomical observations by high-resolution spectroscopy telescopes such as Herschel, SOFIA, and ALMA. The comprehensive experimental rovibrational energy levels reported here will permit further refinement of the potential energy surface to improve ammonia ab initio calculations and facilitate assignment of new high-resolution spectra of hot ammonia.     

Synthesis of β-aminovinylphosphonates by organocatalytic nucleophilic displacement of acetate with amines

The synthesis of diethyl β-aminovinylphosphonates 2 from acetoxy phosphonate 1 is described. The reaction entails an organocatalyzed substitution of the acetoxy group by primary or secondary amines. The use of a catalytic amount of DABCO is necessary if the amine is not nucleophilic enough, otherwise a strong nucleophilic amine can react without organocatalyst. The reaction led to a series of functionalized title compounds in good to excellent yields.     

Ultrafast spectroscopy and computational study of the photochemistry of diphenylphosphoryl azide: direct spectroscopic observation of a singlet phosphorylnitrene

The photochemistry of diphenylphosphoryl azide was studied by femtosecond transient absorption spectroscopy, by chemical analysis of light-induced reaction products, and by RI-CC2/TZVP and TD-B3LYP/TZVP computational methods. Theoretical methods predicted two possible mechanisms for singlet diphenylphosphorylnitrene formation from the photoexcited phosphoryl azide. (i) Energy transfer from the (π,π*) singlet excited state, localized on a phenyl ring, to the azide moiety, thereby leading to the formation of the singlet excited azide, which subsequently loses molecular nitrogen to form the singlet diphenylphosphorylnitrene. (ii) Direct irradiation of the azide moiety to form an excited singlet state of the azide, which in turn loses molecular nitrogen to form the singlet diphenylphosphorylnitrene. Two transient species were observed upon ultrafast photolysis (260 nm) of diphenylphosphoryl azide. The first transient absorption, centered at 430 nm (lifetime (τ) ～ 28 ps), was assigned to a (π,π*) singlet S(1) excited state localized on a phenyl ring, and the second transient observed at 525 nm (τ ～ 480 ps) was assigned to singlet diphenylphosphorylnitrene. Experimental and computational results obtained from the study of diphenyl phosphoramidate, along with the results obtained with diphenylphosphoryl azide, supported the mechanism of energy transfer from the singlet excited phenyl ring to the azide moiety, followed by nitrogen extrusion to form the singlet phosphorylnitrene. Ultrafast time-resolved studies performed on diphenylphosphoryl azide with the singlet nitrene quencher, tris(trimethylsilyl)silane, confirmed the spectroscopic assignment of singlet diphenylphosphorylnitrene to the 525 nm absorption band.     

Evaluation of standard and advanced preprocessing methods for the univariate analysis of blood serum 1H-NMR spectra

Proton nuclear magnetic resonance (¹H-NMR)-based metabolomics enables the high-resolution and high-throughput assessment of a broad spectrum of metabolites in biofluids. Despite the straightforward character of the experimental methodology, the analysis of spectral profiles is rather complex, particularly due to the requirement of numerous data preprocessing steps. Here, we evaluate how several of the most common preprocessing procedures affect the subsequent univariate analyses of blood serum spectra, with a particular focus on how the standard methods perform compared to more advanced examples. Carr–Purcell–Meiboom–Gill 1D ¹H spectra were obtained for 240 serum samples from healthy subjects of the Asklepios study. We studied the impact of different preprocessing steps—integral (standard method) and probabilistic quotient normalization; no, equidistant (standard), and adaptive-intelligent binning; mean (standard) and maximum bin intensity data summation—on the resonance intensities of three different types of metabolites: triglycerides, glucose, and creatinine. The effects were evaluated by correlating the differently preprocessed NMR data with the independently measured metabolite concentrations. The analyses revealed that the standard methods performed inferiorly and that a combination of probabilistic quotient normalization after adaptive-intelligent binning and maximum intensity variable definition yielded the best overall results (triglycerides, R = 0.98; glucose, R = 0.76; creatinine, R = 0.70). Therefore, at least in the case of serum metabolomics, these or equivalent methods should be preferred above the standard preprocessing methods, particularly for univariate analyses. Additional optimization of the normalization procedure might further improve the analyses.