Lipopeptides from the Banyan Endophyte, Bacillus subtilis K1: Mass Spectrometric Characterization of a Library of Fengycins

Mass spectrometric analysis of a banyan endophyte, Bacillus subtilis K1, extract showing broad spectrum antifungal activity revealed a complex mixture of lipopeptides, iturins, surfactins, and fengycins. Fractionation by reversed-phase high performance liquid chromatography (HPLC) facilitated a detailed analysis of fengycin microheterogeneity. Matrix assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) mass spectrometric studies permitted the identification of several new fengycin variants. Four major sites of heterogeneity are identified: (1) N-terminus beta-hydroxy fatty acid moiety, where chain length variation and the presence of unsaturation occur, (2) position 6 (Ala/Val/Ile/Leu), (3) position 10 (Val/Ile) within the macrocyclic ring, and (4) Gln to Glu replacement at position 8, resulting in fengycin variants that differ in mass by 1 Da. Diagnostic fragment ions provide a quick method for localizing the sites of variation in the macrocycle or the linear segment. Subsequent establishment of the sequences is achieved by MS/MS analysis of linear fengycin species produced by hydrolysis of the macrocyclic lactone. Unsaturation in the fatty acid chain and the presence of linear precursors in the B. subtilis K1 extract are also established by mass spectrometry. The anomalous distribution of intensities within isotopic multiplets is a diagnostic for Gln/Glu replacements. High resolution mass spectrometry facilitates the identification of fengycin species differing by 1 Da by localizing the variable position (Gln(8)/Glu(8)) in the fengycin variants.

The Escherichia coli Phosphotyrosine Proteome Relates to Core Pathways and Virulence

While phosphotyrosine modification is an established regulatory mechanism in eukaryotes, it is less well characterized in bacteria due to low prevalence. To gain insight into the extent and biological importance of tyrosine phosphorylation in Escherichia coli, we used immunoaffinity-based phosphotyrosine peptide enrichment combined with high resolution mass spectrometry analysis to comprehensively identify tyrosine phosphorylated proteins and accurately map phosphotyrosine sites. We identified a total of 512 unique phosphotyrosine sites on 342 proteins in E. coli K12 and the human pathogen enterohemorrhagic E. coli (EHEC) O157:H7, representing the largest phosphotyrosine proteome reported to date in bacteria. This large number of tyrosine phosphorylation sites allowed us to define five phosphotyrosine site motifs. Tyrosine phosphorylated proteins belong to various functional classes such as metabolism, gene expression and virulence. We demonstrate for the first time that proteins of a type III secretion system (T3SS), required for the attaching and effacing (A/E) lesion phenotype characteristic for intestinal colonization by certain EHEC strains, are tyrosine phosphorylated by bacterial kinases. Yet, A/E lesion and metabolic phenotypes were unaffected by the mutation of the two currently known tyrosine kinases, Etk and Wzc. Substantial residual tyrosine phosphorylation present in an etk wzc double mutant strongly indicated the presence of hitherto unknown tyrosine kinases in E. coli. We assess the functional importance of tyrosine phosphorylation and demonstrate that the phosphorylated tyrosine residue of the regulator SspA positively affects expression and secretion of T3SS proteins and formation of A/E lesions. Altogether, our study reveals that tyrosine phosphorylation in bacteria is more prevalent than previously recognized, and suggests the involvement of phosphotyrosine-mediated signaling in a broad range of cellular functions and virulence.

High precision Mg isotope measurements of meteoritic samples by secondary ion mass spectrometry

The possibility of establishing an accurate relative chronology of the early solar system events based on the decay of short-lived Al-26 to Mg-26 (half-life of 0.72 Myr) depends on the level of homogeneity (or heterogeneity) of Al-26 and Mg isotopes. However, this level is difficult. to constrain precisely because of the very high precision needed for the determination of isotopic ratios, typically of +/- 5 ppm. In this study, we report for the first time a detailed analytical protocol developed for high precision in situ Mg isotopic measurements ((25)mg/(24)mg and (26)mg/Mg-24 ratios, as well as Mg-26 excess) by MC-SIMS. As the data reduction process is critical for both accuracy and precision of the final isotopic results, factors such as the Faraday cup (FC) background drift and matrix effects on instrumental fractionation have been investigated. Indeed these instrumental effects impacting the measured Mg-isotope ratios can be as large or larger than the variations we are looking for to constrain the initial distribution of Al-26 and Mg isotopes in the early solar system. Our results show that they definitely are limiting factors regarding the precision of Mg isotopic compositions, and that an under- or over-correction of both FC background instabilities and instrumental isotopic fractionation leads to important bias on delta Mg-25, delta(26)mg and Delta Mg-26 values (for example, olivines not corrected for FC background drifts display Delta Mg-26 values that can differ by as much as 10 ppm from the truly corrected value). The new data reduction process described here can then be applied to meteoritic samples (components of chondritic meteorites for instance) to accurately establish their relative chronology of formation.

Reactive Pulsed Laser Deposition of titanium nitride thin film: Optimization of process parameters using Secondary Ion Mass Spectrometry

Reactive Pulsed Laser Deposition is a single step process wherein the ablated elemental metal reacts with a low pressure ambient gas to form a compound. We report here a Secondary Ion Mass Spectrometry based analytical methodology to conduct minimum number of experiments to arrive at optimal process parameters to obtain high quality TiN thin film. Quality of these films was confirmed by electron microscopic analysis. This methodology can be extended for optimization of other process parameters and materials. (C) 2009 Elsevier B.V. All rights reserved.

Quantitation and characterization of glutathionyl haemoglobin as an oxidative stress marker in chronic renal failure by mass spectrometry

Objectives: Glutathionyl haemoglobin (GS-Hb) belonging to the class of glutathionylated proteins has been investigated as a possible marker of oxidative stress in different chronic diseases. The purpose of this study was to examine whether glutathionyl haemoglobin can serve as an oxidative stress marker in non-diabetic chronic renal failure patients on different renal replacement therapies (RRT) through its quantitation, and characterization of the specific binding site of glutathione in haemoglobin molecule by mass spectrometric analysis. Design and methods: The study group consisted of non-diabetic chronic renal failure patients on renal replacement therapy (RRT): hemodialysis (HD), continuous ambulatory peritoneal dialysis (CAPD) and renal allograft transplant (Txp) patients. Haemoglobin samples of these subjects were analyzed by liquid chromatography electrospray ionization mass spectrometry for GS-Hb quantitation. Characterization of GS-Hb was done by tandem mass spectrometry. Levels of erythrocyte glutathione (GSH) and lipid peroxidation (as thiobarbituric acid reacting substances) were measured spectrophotometrically, while glycated baernoglobin (HbA1c) was measured by HPLC. Results: GS-Hb levels were markedly elevated in the dialysis group and marginally in the transplant group as compared to the controls. GS-Hb levels correlated positively with lipid peroxidation and negatively with the erythrocyte glutathione levels in RRT groups indicating enhanced oxidative stress. De novo sequencing of the chymotryptic fragment of GS-Hb established that glutathione is attached to Cys-93 of the beta globin chain. Mass spectrometric quantitation of total glycated haemoglobin showed good agreement with HbA1c estimation by conventional HPLC method. Conclusions: Glutathionyl haemoglobin can serve as a clinical marker of oxidative stress in chronic debilitating therapies like RRT. Mass spectrometry provides a reliable analytical tool for quantitation and residue level characterization of different post-translational modifications of haemoglobin. (c) 2007 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Detection of alpha(2u)-globulin and its bound putative pheromones in the preputial gland of the Indian commensal rat (Rattus rattus) using mass spectrometry

The role of pheromones and pheromone-binding proteins in the laboratory rat has been extensively investigated. However, we have previously reported that the preputial gland of the Indian commensal rat produces a variety of pheromonal molecules and preputial glands would seem to be the predominant source for pheromonal communication. The presence of pheromone-binding proteins has not yet been identified in the preputial gland of the Indian commensal rat; therefore, the experiments were designed to unravel the alpha(2u)-globulin (alpha 2u) and its bound volatiles in the commensal rat. Total preputial glandular proteins were first fractionated by sodium dodecyl sulfate/polyacrylamide gel electrophoresis (SDS-PAGE) and subsequently analyzed by mass spectrometry. Further, we purified alpha 2u and screened for the presence of bound pheromonal molecules with the aid of gas chromatography/mass spectrometry (GC/MS). A novel alpha 2u was identified with a high score and this protein has not been previously described as present in the preputial gland of Indian commensal rats.This novel alpha 2u was then characterized by tandem mass spectrometry (MS/MS). Peptides with m/z values of 969, 1192, 1303 and 1876 were further fragmented with the aid of MS/MS and generated de novo sequences which provided additional evidence for the presence of alpha 2u in the preputial gland. Finally, we identified the presence of farnesol 1 and 2 bound to alpha 2u. The present investigation confirms the presence of alpha 2u (18.54 kDa) in the preputial gland of the Indian commensal rat and identifies farnesol 1 and 2 as probably involved in chemo-communication by the Indian commensal rat.Copyright (C) 2010 John Wiley & Sons, Ltd.

Sequencing of T-superfamily conotoxins from Conus virgo: Pyroglutamic acid identification and disulfide arrangement by MALDI mass spectrometry

De novo mass spectrometric sequencing of two Conus peptides, Vi1359 and Vi1361, from the vermivorous cone snail Conus virgo, found off the southern Indian coast, is presented. The peptides, whose masses differ only by 2 Da, possess two disulfide bonds and an amidated C-terminus. Simple chemical modifications and enzymatic cleavage coupled with matrix assisted laser desorption ionization (MALDI) mass spectrometric analysis aided in establishing the sequences of Vi1359, ZCCITIPECCRI-NH2, and Vi1361, ZCCPTMPECCRI-NH2, Which differ only at residues 4 and 6 (Z = pyroglutamic acid). The presence of the pyroglutamyl residue at the N-terminus was unambiguously identified by chemical hydrolysis of the cyclic amide, followed by esterification. The presence of Ile residues in both the peptides was confirmed from high-energy collision induced dissociation (CID) studies, using the observation Of W-n- and d(n)-ions as a diagnostic. Differential cysteine labeling, in conjunction with MALDI-MS/MS, permitted establishment of disulfide connectivity in both peptides as Cys2-Cys9 and Cys3-Cys10. The cysteine pattern clearly reveals that the peptides belong to the class of T-superfamily conotoxins, in particular the T-1 superfamily.

Displacement Amplifying Compliant Mechanisms for Two-axis High-resolution Monolithic Inertial Sensors

Novel designs for two-axis, high-resolution, monolithic inertial sensors are presented in this paper. Monolithic, i.e., joint-less single-piece compliant designs are already common in micromachined inertial sensors such as accelerometers and gyroscopes. Here, compliant mechanisms are used not only to achieve de-coupling between motions along two orthogonal axes but also to amplify the displacements of the proof-mass. Sensitivity and resolution capabilities are enhanced because the amplified motion is used for sensing the measurand. A particular symmetric arrangement of displacement-amplifying compliant mechanisms (DaCMs) leads to de-coupled and amplified motion. An existing DaCM and a new topology-optimized DaCM are presented as a building block in the new arrangement. A spring-mass-lever model is presented as a lumped abstraction of the new arrangement. This model is useful for arriving at the optimal parameters of the DaCM and for performing system-level simulation. The new designs improved the performance by a factor of two or more.

The upper Bay of Bengal salinity structure in a high-resolution model

Salinity in the Bay of Bengal is highly heterogeneous, with extremely fresh waters found at the surface in the Northern part of the basin, and saltier waters at subsurface as well as to the south. This paper investigates the seasonal structure of sea surface salinity of the Bay in a regional high-resolution model forced by ERA-Interim reanalysis and various precipitation products. Surface circulation is believed to drive the spreading of northern Bay of Bengal fresh waters to the rest of the Indian Ocean. We first present a series of experiments to infer the sensitivity of modeled circulation to various numerical choices. Surface circulation is found to be sensitive to the horizontal resolution of the model, with the 1/12 degrees version appearing much more realistic than the 1/4 degrees version. The sidewall boundary condition is also drastically influencing the characteristics of the western boundary current simulated. We then investigate the sensitivity of the salinity response to the various precipitation products. We observe that ERA-Interim excess precipitation induces a fresh bias in the surface salinity response. Spaceborne precipitation products are more satisfactory. We then identify the pathways of the northern Bay freshwater mass, based on passive tracers experiments. Our model suggests that over timescales of a few months, vertical exchanges between the upper fresh layer and the underlying saltier layer appear to be the main export pathway for the freshwater. The horizontal circulation within the mixed layer also acts to convey fresh waters out of the Bay at these timescales, but in a lesser quantity compared to the vertical export. Beyond its intrinsic interest for the understanding of Bay of Bengal physics, this study highlights the need for a careful design of any realistic numerical model, in three key aspects: the choice of the resolution of the model, the choice of the sub-grid scale parameterizations, and the choice of the forcing fluxes. (C) 2013 Elsevier Ltd. All rights reserved.

Mass spectrometry based characterization of Hb Beckman variant in a falsely elevated HbA(1c) sample

Glycated hemoglobin (HbA(1c)) is a `gold standard' biomarker for assessing the glycemic index of an individual. HbA(1c) is formed due to nonenzymatic glycosylation at N-terminal valine residue of the P-globin chain. Cation exchange based high performance liquid chromatography (CE HPLC) is mostly used to quantify HbA(1c), in blood sample. A few genetic variants of hemoglobin and post-translationally modified variants of hemoglobin interfere with CE HPLC-based quantification,. resulting in its false positive estimation. Using mass spectrometry, we analyzed a blood sample with abnormally high HbA(1c) (52.1%) in the CE HPLC method. The observed HbA(1c) did not corroborate the blood glucose level of the patient. A mass spectrometry based bottom up proteomics approach, intact globin chain mass analysis, and chemical modification of the proteolytic peptides identified the presence of Hb Beckman, a genetic variant of hemoglobin, in the experimental sample. A similar surface area to charge ratio between HbA(1c) and Hb Beckman might have resulted in the coelution of the variant with HbA(1c) in CE HPLC. Therefore, in the screening of diabetes mellitus through the estimation of HbA(1c), it is important to look for genetic variants of hemoglobin in samples that show abnormally high glycemic index, and HbA(1c) must be estimated using an alternative method. (C) 2015 Elsevier Inc. All rights reserved.

Luffa acutangula agglutinin: Primary structure determination and identification of a tryptophan residue involved in its carbohydrate-binding activity using mass spectrometry

A lectin from phloem exudates of Luffa acutangula (ridge gourd) was purified on chitin affinity chromatography and characterized for its amino acid sequence and to study the role of tryptophan in its activity. The purified lectin was subjected to various proteolytic digestions, and the resulting peptides were analyzed by liquid chromatography coupled electrospray ionization ion trap mass spectrometer. The peptide precursor ions were fragmented by collision-induced dissociation or electron transfer dissociation experiments, and a manual interpretation of MS/MS was performed to deduce amino acid sequence. This gave rise to almost complete sequence coverage of the lectin which showed high-sequence similarity with deduced sequences of phloem lectins present in the database. Chemical modification of lysine, tyrosine, histidine, arginine, aspartic acid, and glutamic acid residues did not inhibit the hemagglutinating activity. However, the modification of tryptophan residues using N-bromosuccinimide showed the loss of hemagglutinating activity. Additionally, the mapping of tryptophan residues was performed to determine the extent and number of residues modified, which revealed that six residues per molecule were oxidized suggesting their accessibility. The retention of the lectin activity was seen when the modifications were performed in the presence of chitooligosaccharides due to protection of a tryptophan residue (W-102) in the protein. These studies taken together have led to the identification of a particular tryptophan residue (W-102) in the activity of the lectin. (c) 2015 IUBMB Life, 67(12):943-953, 2015

A High-Resolution Transmission of the Precipitation Process in a Electron Microscopy Study Dilute Ti-N Alloy

The precipitation processes in dilute nitrogen alloys of titanium have been examined in detail by conventional transmission electron microscopy (CTEM) and high-resolution electron microscopy (HREM). The alloy Ti-2 at. pct N on quenching from its high-temperature beta phase field has been found to undergo early stages of decomposition. The supersaturated solid solution (alpha''-hcp) on decomposition gives rise to an intimately mixed, irresolvable product microstructure. The associated strong tweed contrast presents difficulties in understanding the characteristic features of the process. Therefore, HREM has been carried out with a view to getting a clear picture of the decomposition process. Studies on the quenched samples of the alloy suggest the formation of solute-rich zones of a few atom layers thick, randomly distributed throughout the matrix. On aging, these zones grow to a size beyond which the precipitate/matrix interfaces appear to become incoherent and the alpha' (tetragonal) product phase is seen distinctly. The structural details, the crystallography of the precipitation process, and the sequence of precipitation reaction in the system are illustrated.

High-resolution refinement of orthorhombic bovine pancreatic phospholipase A2

The X-ray structure of recombinant bovine pancreatic phospholipase A(2) (PLA2), which specifically catalyzes the cleavage of the sn-2 acylester bond of phospholipids, has been refined at 1.5 Angstrom resolution. The crystal belongs to the space group P2(1)2(1)2(1) with unit-cell parameters a = 47.12, b = 64.59 and c = 38.14 Angstrom similar to the native enzyme reported previously by Dijkstra et nl. [J. Mel. Biol. (1981), 147, 97-123]. The refinement converged to an R value of 18.4% (R-free = 22.8%) for 16 374 reflections between 10.0 and 1.5 Angstrom resolution. The surface-loop residues (60-70) art: ordered in the present orthorhombic recombinant enzyme, but disordered in the trigonal recombinant enzyme. The active-site residues, His48, Asp99, and the catalytic water superimpose well with the trigonal form. Besides the catalytic water which is hydrogen bonded to His48, it is often seen that there is a second water attached to the same N atom of His48 and simultaneously hydrogen bonded to the O atom of Asp49. It is thought that the second water facilitates the tautomerism of His48 for enzyme catalysis, The catalytic water is also hydrogen bonded to the equatorial water coordinated to the calcium ion, In addition to the equatorial water, there is also an axial calcium water and the additional structural water. These five common water molecules are hydrogen bonded to the additional 16 water molecules in the present orthorhombic structure which may further enhance the structural integrity of the active site. Besides the protein and one calcium ion, a total of 134 water molecules were located in the present high-resolution refinement.

Crop Classification using Biologically-inspired Techniques with High Resolution Satellite Image

Remote sensing provides a lucid and effective means for crop coverage identification. Crop coverage identification is a very important technique, as it provides vital information on the type and extent of crop cultivated in a particular area. This information has immense potential in the planning for further cultivation activities and for optimal usage of the available fertile land. As the frontiers of space technology advance, the knowledge derived from the satellite data has also grown in sophistication. Further, image classification forms the core of the solution to the crop coverage identification problem. No single classifier can prove to satisfactorily classify all the basic crop cover mapping problems of a cultivated region. We present in this paper the experimental results of multiple classification techniques for the problem of crop cover mapping of a cultivated region. A detailed comparison of the algorithms inspired by social behaviour of insects and conventional statistical method for crop classification is presented in this paper. These include the Maximum Likelihood Classifier (MLC), Particle Swarm Optimisation (PSO) and Ant Colony Optimisation (ACO) techniques. The high resolution satellite image has been used for the experiments.

Robust and High-resolution Voiced/Unvoiced Classification in Noisy Speech Using A Signal Smoothness Criterion

We propose a novel technique for robust voiced/unvoiced segment detection in noisy speech, based on local polynomial regression. The local polynomial model is well-suited for voiced segments in speech. The unvoiced segments are noise-like and do not exhibit any smooth structure. This property of smoothness is used for devising a new metric called the variance ratio metric, which, after thresholding, indicates the voiced/unvoiced boundaries with 75% accuracy for 0dB global signal-to-noise ratio (SNR). A novelty of our algorithm is that it processes the signal continuously, sample-by-sample rather than frame-by-frame. Simulation results on TIMIT speech database (downsampled to 8kHz) for various SNRs are presented to illustrate the performance of the new algorithm. Results indicate that the algorithm is robust even in high noise levels.