Redetermination of the X-ray structure of nitroxylcobalamin: base-on nitroxylcobalamin exhibits a remarkably long Co-N(dimethylbenzimidazole) bond distance

The X-ray structures of three new crystals of nitroxylcobalamin (NOCbl) have been determined. Unlike our earlier reported structure in which NOCbl was partially oxidized (L. Hannibal, C. A. Smith, D. W. Jacobsen and N. E. Brasch, Angew. Chem., Int. Ed. 2007, 46, 5140), the O atom of the nitroxyl ligand is located in a single position with a N=O bond distance of 1.12-1.14 ?, consistent with a double bond. The Co-N-O angle is in the 118.9-120.3 ? range. The α-axial Co-N(dimethylbenzimidazole) (Co-NB3) bond distance is a remarkable 2.32-2.35 ? in length, ~0.1 ? longer than that reported for all other cobalamin structures. The change in the Gibbs free energy for the base-on/base-off equilibrium now correlates extremely well with the Co-NB3 bond distance, as observed for other cobalamins.     

A top-down LC-FTICR MS-based strategy for characterizing oxidized calmodulin in activated macrophages

A liquid chromatography-mass spectrometry (LC-MS)-based approach for characterizing the degree of nitration and oxidation of intact calmodulin (CaM) has been used to resolve ～250 CaM oxiforms using only 500 ng of protein. The analysis was based on high-resolution data of the intact CaM isoforms obtained by Fourier-transform ion cyclotron resonance mass spectrometry (FTICR MS) coupled with an on-line reversed-phase LC separation. Tentative identifications of post-translational modifications (PTMs), such as oxidation or nitration, have been assigned by matching observed protein mass to a database containing all theoretically predicted oxidation products of CaM and verified through a combination of tryptic peptide information (generated from bottom-up analyses) and on-line collisionally induced dissociation (CID) tandem mass spectrometry (MS/MS) at the intact protein level. The reduction in abundance and diversity of oxidatively modified CaM (i.e., nitrated tyrosines and oxidized methionines) induced by macrophage activation has been explored and semiquantified for different oxidation degrees (i.e., no oxidation, moderate, and high oxidation). This work demonstrates the power of the top-down approach to identify and quantify hundreds of combinations of PTMs for single protein target such as CaM and implicate competing repair and peptidase activities to modulate cellular metabolism in response to oxidative stress.     

An efficient data format for mass spectrometry-based proteomics

The diverse range of mass spectrometry (MS) instrumentation along with corresponding proprietary and nonproprietary data formats has generated a proteomics community driven call for a standardized format to facilitate management, processing, storing, visualization, and exchange of both experimental and processed data. To date, significant efforts have been extended towards standardizing XML-based formats for mass spectrometry data representation, despite the recognized inefficiencies associated with storing large numeric datasets in XML. The proteomics community has periodically entertained alternate strategies for data exchange, e.g., using a common application programming interface or a database-derived format. However, these efforts have yet to gain significant attention, mostly because they have not demonstrated significant performance benefits over existing standards, but also due to issues such as extensibility to multidimensional separation systems, robustness of operation, and incomplete or mismatched vocabulary. Here, we describe a format based on standard database principles that offers multiple benefits over existing formats in terms of storage size, ease of processing, data retrieval times, and extensibility to accommodate multidimensional separation systems.     

Identification of candidate biomarkers in ovarian cancer serum by depletion of highly abundant proteins and differential in‐gel electrophoresis

Ovarian cancer is the fifth leading cause of cancer death for women in the US, yet survival rates are over 90% when it is diagnosed at an early stage, highlighting the need for biomarkers for early detection. To enhance the discovery of tumor‐specific proteins that could represent novel serum biomarkers for ovarian cancer, we depleted serum of highly abundant proteins which can mask the detection of proteins present in serum at low concentrations. Three commercial immunoaffinity columns were used in parallel to deplete the highly abundant proteins in serum from 60 patients with serous ovarian carcinoma and 60 non‐cancer controls. Medium and low abundance serum proteins from each serum pool were then evaluated by the quantitative proteomic technique of differential in‐gel electrophoresis. The number of protein spots that were elevated in ovarian cancer sera by at least twofold ranged from 36 to 248, depending upon the depletion and separation methods. From the 33 spots picked for MS analysis, nine different proteins were identified, including the novel candidate ovarian cancer biomarkers leucine‐rich α2 glycoprotein‐1 and ficolin 3. Western blotting validated the relative increases in serum protein levels for three of the proteins identified, demonstrating the utility of this approach for the identification of novel serum biomarkers for ovarian cancer.     

Anodic film formation on binary Al?Mg and Al?Ti alloys in nitric acid

Nitric acid is commonly used for surface treatments of aluminium alloys. It is used to clean the surfaces after alkaline etching; it has application in chemical polishing and is also used for electrograining. The majority of these treatments undergo the application of anodic polarisation that results in formation of anodic oxide film. However, little is known about the behaviour of aluminium containing magnesium or titanium in solid solution under such conditions. To reveal the effects of magnesium and titanium alloying additions on anodic film formation in nitric acid, Al‐1800 ppm Mg and Al‐800 ppm Ti alloys were investigated. It was found that porous alumina film developed on the surfaces with reduced efficiency of 40%, due to the reactive nature of nitric acid to alumina. The presence of magnesium and titanium in aluminium had little influence on the efficiency of film growth, as confirmed by the relatively similar thicknesses of oxide formed on binary alloys and aluminium. However, incorporation of magnesium ions into the alumina film led to development of a high‐population density of localised voids near the alloy/film interface. An increased titanium content was found in the film regions close to the alloy/film interface, indicating its oxidation. Copyright © 2009 John Wiley & Sons, Ltd.     

An automated instrument for human STR identification: design, characterization, and experimental validation

The microfluidic integration of an entire DNA analysis workflow on a fully integrated miniaturized instrument is reported using lab‐on‐a‐chip automation to perform DNA fingerprinting compatible with CODIS standard relevant to the forensic community. The instrument aims to improve the cost, duration, and ease of use to perform a “sample‐to‐profile” analysis with no need for human intervention. The present publication describes the operation of the three major components of the system: the electronic control components, the microfluidic cartridge and CE microchip, and the optical excitation/detection module. Experimental details are given to characterize the level of performance, stability, reliability, accuracy, and sensitivity of the prototype system. A typical temperature profile from a PCR amplification process and an electropherogram of a commercial size standard (GeneScan 500?, Applied Biosystems) separation are shown to assess the relevance of the instrument to forensic applications. Finally, we present a profile from an automated integrated run where lysed cells from a buccal swab were introduced in the system and no further human intervention was required to complete the analysis.     

Accurate particle size distribution determination by nanoparticle tracking analysis based on 2-D Brownian dynamics simulation

A physical model is presented to simulate the average step length distribution during nanoparticle tracking analysis experiments as a function of the particle size distribution and the distribution of the number of steps within the tracks. Considering only tracks of at least five steps, numerical simulation could be replaced by a normal distribution approximation. Based on this model, simulation of a step length distribution allows obtaining a much more reliable estimation of the particle size distribution, thereby reducing the artificial broadening of the distribution, as is typically observed by direct conversion of step length to particle size data. As this fitting procedure also allowed including data from particles that were followed for a relatively low number of steps, the measurement time could be reduced for particles that are known to be monodisperse. Whereas the inversion is less sensitive towards the particle size distribution width, still similar values were obtained for both the average diameter and standard deviation of a polystyrene latex sample irrespective of the track length, provided that the latter included at least five steps.     

Investigation of copper oxide impregnants prepared from various precursors for respirator carbons

Copper oxide impregnated activated carbon was prepared by three methods and studied as a respirator carbon. Using techniques such as dynamic flow testing, X-ray diffraction (XRD), thermal analysis, scanning electron microscopy (SEM) and energy dispersive X-ray analysis (EDX), copper oxide impregnants, derived from different sources such as basic copper carbonate (Cu₂CO₃(OH)₂), copper nitrate (Cu(NO₃)₂) and copper chloride (CuCl₂) reacted with sodium hydroxide (NaOH), have been studied. Dynamic flow tests performed using sulfur dioxide (SO₂), ammonia (NH₃) and hydrogen cyanide (HCN) challenge gases allow the determination of the stoichiometric ratio of reaction (SRR) between challenge gas and impregnant. Thermal gravimetric analysis experiments showed that an inert heating environment was required when thermally decomposing the Cu(NO₃)₂ impregnant to CuO to avoid damaging the activated carbon substrate. SEM has been used to investigate dispersal and particle size of the impregnant on the activated carbon. XRD permits the identification of crystalline and amorphous phases as well as the grain size of the impregnant. XRD analysis of samples before and after exposure to SO₂ has allowed the active impregnant in SO₂ adsorption to be identified. The relationship between SRR, impregnant loading and grain size is discussed. Methods to improve impregnant distribution are presented and their impact discussed.     

Highlighting the possible secondary interactions in the role of balhimycin and its analogues for enantiorecognition in capillary electrophoresis

It is believed that the enantiorecognition mechanism based on macrocyclic antibiotics involves multimodal interactions via hydrogen bonding, π–π interaction, steric hindrance, hydrophobic interaction and so on. A variety of enantiomeric N-benzoylated amino acids were separated using balhimycin (A) or its analogues bromobalhimycin (B) and dechlorobalhimycin (C) as chiral mobile phase additive using a CE method, which combined the partial filling technique with the dynamic coating technique and the co-EOF electrophoresis technique. The enantioresolution and the migration time were highly relevant to the structure of analytes, especially to the substitutions on the N-tagged benzoyl moiety of the amino acids. A steric effect and π–π interaction based mechanism is proposed in order to explain some observed enantioresolution differences between positional isomers. Notably dechlorobalhimycin exhibited the best enantioresolution for several N-benzoylated derivatives of leucine, which was rarely observed for N-dansylated amino acid derivatives. The hydrophobicity difference of the aglycone pocket among three chiral selectors was assumed to account for this behaviour.