Low-molecular-weight human serum proteome using ultrafiltration, isoelectric focusing, and mass spectrometry

Identification of the serum proteome is a daunting analytical task due to the complex nature of the sample which has an extremely large dynamic range of protein components. This report addresses this issue by using centrifugal ultrafiltration to enrich the low-molecular-weight (LMW) serum proteome while decreasing the amount of abundant high-molecular-weight proteins. Reduction of the complex nature of the sample was achieved by fractionation of the LMW serum proteins using solution-phase isoelectric focusing (IEF). Multiple enzyme digestions are performed and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Analysis of the tandem mass spectra resulted in the identification of 262 proteins belonging to LMW serum proteome. Our results demonstrate the effectiveness of this methodology to isolate and identify LMW proteins with improved confidence in the MS data acquired. In addition, our methodology can be combined with other multidimensional chromatography techniques performed on the peptide level to increase the number of identified proteins.     

Phase diagram and phase transitions of Krypton on graphite in the extended monolayer regime

We report high resolution x-ray diffraction studies of the structures and phase transitions of monolayer krypton, adsorbed on both powder and single crystal graphite substrates. A comprehensive series of powder diffraction profiles is used to construct the two dimensional phase diagram. The melting of the commensurate solid is shown to be strongly first order throughout the region where tricritical behavior was previously thought to occur; fluid solid coexistence extends up to the termination of the commensurate phase at 130 K. A disordered weakly incommensurate phase is shown to be a reentrant fluid, a system which may be described as a disordered network of domain walls and which evolves continuously into a more conventional 2D fluid. This evolution is marked by the disappearance of satellite peaks which are caused by the modulation of the overlayer by the substrate. The freezing of the reentrant fluid into the commensurate phase is shown to be consistent with a chiral Potts transition, its freezing into the incommensurate solid consistent with a dislocation binding transition.Single crystal experiments reveal the orientation of the weakly incommensurate phase. The reentrant fluid is found to have no visible orientational fluctuations, manifesting isotropic diffraction peaks. This is attributed to the strong epitaxy of domain walls. The incommensurate solid is shown to undergo an aligned-rotated transition which is well described by zerotemperature calculations.     

Synthesis and biological evaluation of analogues of the antibiotic pantocin B

Strains of the bacteria Erwinia herbicola produce antibiotics that effectively control E. amylovora, the bacterial pathogen responsible for the plant disease fire blight. Pantocin B was the first of these antibiotics to be characterized, and a flexible synthesis of various analogues is reported. Embedded in the "pseudo-tripeptide" backbone of pantocin B are a methylenediamine and a methyl sulfone, both unusual structural features in natural products. The peptidic nature of pantocin B facilitated a series of structure-activity relationship studies that probed the roles of these functional groups in determining the biological activity of pantocin B. A clear demarcation of the roles between the N- and C-terminal portions of the antibiotic was determined as a result of the structure-activity relationship studies. The N-terminal L-alanyl group is needed for cellular import but not for interaction with the intracellular target, the arginine biosynthetic enzyme N-acetylornithine aminotransferase. The methylenediamine and methyl sulfone portions were found to be essential for antibiotic activity, presumably due to extensive interactions with N-acetylornithine aminotransferase.     

Mass spectrometry of polycyclic tetracarboxylic ('ARN') acids and tetramethyl esters

Polycyclic C(80) tetracarboxylic (so-called 'ARN') acids are found as calcium salts in deposits which form in certain oilfield pipelines and equipment. Characterisation of these acids is important for improving the prediction and hence avoidance or minimisation of oilfield deposition problems. Although several of the acids have been isolated and characterised (as regioisomeric mixtures) by nuclear magnetic resonance spectroscopy, mass spectrometric methods are likely to be much more useful for the routine analysis of oils and deposits containing the acids. A publication summarising the mass spectra of the purified acids and major derivatives might thus be a very useful source of reference for scientists and technologists studying these unusual compounds. We now report the characterisation of several of the purified acids and of the tetramethyl esters by electrospray ionisation mass spectrometry (ESI-MS) in both positive ion and negative ion modes, by multistage ESI-MS with a suggested rationalisation of the ions produced, by positive ion atmospheric solids analysis probe (ASAP) atmospheric pressure chemical ionisation (APCI), and by positive ion electron ionisation (EI)-MS. Tentative identifications of C(80) acyclic, mono-, bi- and tricylic tetraacids and the δ(13)C isotope values of a mixture of the semi-pure acids determined by MS are also reported for the first time.     

Optimization of N‐methyl‐N‐[tert‐butyldimethylsilyl]trifluoroacetamide as a derivatization agent for determining isotopic enrichment of glycerol in very‐low density lipoproteins

Stable isotope kinetic studies play an important role in the study of very‐low density lipoprotein (VLDL) metabolism, including basic and clinical research. Today, [1,1,2,3,3‐²H₅]glycerol is the most cost‐effective alternative to measure glycerol and triglyceride kinetics. Recycling of glycerol from glycolysis and gluconeogenesis may lead to incompletely labelled tracer molecules. Many existing methods for the measurement of glycerol isotopic enrichment involve the production of glycerol derivatives that result in fragmentation of the glycerol molecule after ionization. It would be favourable to measure the intact tracer molecule since incompletely labelled tracer molecules may be measured as fully labelled. The number of methods available to measure the intact tracer in biological samples is limited. The aim of this project was to develop a gas chromatography/mass spectrometry (GC/MS) method for glycerol enrichment that measures the intact glycerol backbone and is suitable for electron ionization (EI), which is widely available. A previously published method for N‐methyl‐N‐[tert‐butyldimethylsilyl]trifluoroacetamide (MTBSTFA) derivatization was significantly improved; we produced a stable derivative and increased recovery 27‐fold in standards. We used the optimized MTBSTFA method in VLDL‐triglyceride and found that further modification was required to take matrix effects into account. We now have a robust method to measure glycerol isotopic enrichment by GC/EI‐MS that can be used to rule out the known problem of tracer recycling in studies of VLDL kinetics. Copyright © 2010 John Wiley & Sons, Ltd.     

Are the structures of twist grain boundaries in silicon ordered at 0 K?

Contrary to previous simulation results on the existence of amorphous intergranular films at high-angle twist grain boundaries (GBs) in elemental solids such as silicon, recent experimental results imply structural order in some high-angle boundaries. With a novel protocol for simulating twist GBs, which allows the number of atoms at the boundary to vary, we have found new low-energy ordered structures. We give a detailed exposition of the results for the simplest boundary. The validity of our results is confirmed by first-principles calculations.     

Testing the Pauli exclusion principle with the NEMO-2 detector

The Pauli Exclusion Principle (PEP) was tested with the NEMO-2 detector. Limits at the 90% C.L. on the violation of PEP for p-shell nucleons in ¹²C were obtained. Specifically, transitions to the fully occupied 1s _1/2-shell yielded a limit of 4.2 · 10²⁴ y for the process with emission of a γ-quantum. Similarly limits of 3.1 · 10²⁴ y for β⁻ and 2.6 · 10²⁴ y for β⁺ Pauli-forbidden transitions of ¹²C →¹²?¹²B) are reported here. Received: 25 August 1999     

New tandem catalysis: preparation of cyclic enol ethers through a ruthenium-catalyzed ring-closing metathesis-olefin isomerization sequence

Tandem reactions that proceed with a single metal catalyst precursor offer novel opportunities for developing efficient new reaction sequences. In this regard, reaction conditions have been identified that allows for a tandem ring-closing metathesis-olefin isomerization sequence catalyzed by a common ruthenium precursor. Specifically, the tandem process generates cyclic enol ethers from a variety of readily available acyclic dienes in a single reaction vessel using Grubbs' ruthenium alkylidene.