Mining the human plasma proteome with three-dimensional strategies by high-resolution Quadrupole Orbitrap Mass Spectrometry

Human plasma is a readily available clinical sample that reflects the status of the body in normal physiological and disease states. Although the wide dynamic range and immense complexity of plasma proteins are obstacles, comprehensive proteomic analysis of human plasma is necessary for biomarker discovery and further verification. Various methods such as immunodepletion, protein equalization and hyper fractionation have been applied to reduce the influence of high-abundance proteins (HAPs) and to reduce the high level of complexity. However, the depth at which the human plasma proteome has been explored in a relatively short time frame has been limited, which impedes the transfer of proteomic techniques to clinical research. Development of an optimal strategy is expected to improve the efficiency of human plasma proteome profiling.     

Model-guided metabolic gene knockout of gnd for enhanced succinate production in Escherichia coli from glucose and glycerol substrates

The metabolic role of 6-phosphogluconate dehydrogenase (gnd) under anaerobic conditions with respect to succinate production in Escherichia coli remained largely unspecified. Herein we report what are to our knowledge the first metabolic gene knockout of gnd to have increased succinic acid production using both glucose and glycerol substrates in E. coli. Guided by a genome scale metabolic model, we engineered the E. coli host metabolism to enhance anaerobic production of succinic acid by deleting the gnd gene, considering its location in the boundary of oxidative and non-oxidative pentose phosphate pathway. This strategy induced either the activation of malic enzyme, causing up-regulation of phosphoenolpyruvate carboxylase (ppc) and down regulation of phosphoenolpyruvate carboxykinase (ppck) and/or prevents the decarboxylation of 6 phosphogluconate to increase the pool of glyceraldehyde-3-phosphate (GAP) that is required for the formation of phosphoenolpyruvate (PEP). This approach produced a mutant strain BMS2 with succinic acid production titers of 0.35 g l⁻¹ and 1.40 g l⁻¹ from glucose and glycerol substrates respectively. This work further clearly elucidates and informs other studies that the gnd gene, is a novel deletion target for increasing succinate production in E. coli under anaerobic condition using glucose and glycerol carbon sources. The knowledge gained in this study would help in E. coli and other microbial strains development for increasing succinate production and/or other industrial chemicals.     

Liquid chromatography with mass spectrometry and NMR spectroscopy based discovery of cytotoxic principles from Daphne tangutica Maxim

An ethyl acetate extract from the barks of the ethnic Chinese medicine Daphne tangutica Maxim. exhibited antihepatocellular carcinoma activity against HepG2 and Hep3B cell lines. By using high‐performance liquid chromatography based activity profiling in combination with offline liquid chromatography with mass spectrometry and NMR analysis, we rapidly identified ten major components of the extract, including seven active principles, coumarins ( 1–4 ) and biscoumarins ( 7, 8, 10 ), along with three inactive flavonoids ( 5, 6, 9 ). This study demonstrated that our combined protocol can be used as an important strategy for chemical profiling, dereplication as well as the identification of bioactive compounds from herbal medicines.     

Profiling of amine metabolites in human biofluids by micellar electrokinetic chromatography with laser-induced fluorescence detection

A rapid and sensitive capillary electrophoresis (CE) method has been developed for profiling organic metabolites containing amine functional groups in mammalian biofluids. Metabolites containing an amine group were derivatized with 4-fluoro-7-nitrobenzo-2,1,3-oxadiazol (NBD-F), separated by micellar electrokinetic chromatography (MEKC), and detected by argon-ion (488 nm) laser-induced fluorescence detection. The optimized MEKC background electrolyte conditions were: 50 mmol L⁻¹ sodium cholate, 5 mmol L⁻¹ β-cyclodextrin, and 20 mmol L⁻¹ Brij 35 in 20 mmol L⁻¹ aqueous borate buffer, pH 9.3, containing 7% methanol. Under these conditions all the amine compounds in mammalian biofluids, for example plasma, saliva, and urine, were derivatized directly, without extraction, in a minimum volume of 100 nL and the derivatives could be separated within 16 min. Up to 90% of the amine-containing metabolites in plasma and saliva could be identified by reference to standard compounds. For twenty amine standards linearity of calibration was better than R ² = 0.99. Migration-time and peak-area reproducibility were better than RSD 1.5% and 15% respectively. In replicate analysis of human plasma bioanalytical precision ranged between 0.7 and 3.8 RSD% for a 5.0-μL volume and between 1.7 and 5.5 RSD% for 100-nL volume. The concentrations measured were found to be in agreement with literature values.     

Analysis of catecholamines and related compounds in one whole metabolic pathway with high performance liquid chromatography based on derivatization

The simultaneous determination of Tyr, catecholamines and their metabolites in one whole metabolic pathway using high performance liquid chromatography coupled with fluorescence detection (HPLC–FLD) based on pre-column derivatization has been achieved successfully. 1,3,5,7-Tetramethyl-8-(N-hydroxysuccinimidyl butyric ester)-difluoroboradiaza-s-indacene (TMBB-Su), a highly reactive fluorescent reagent synthesized in our previous work, was used for the labeling of tyrosine (Tyr), l-3,4-dihydroxyphenylalanine (l-DOPA), dopamine (DA), norepinephrine (NE), epinephrine (E) and metanephrine (MN). Derivatization conditions including reagent concentration, buffer, reaction temperature and reaction time were also investigated to improve the derivatization efficiency and thus the sensitivity of the detection. The separation of the derivatives was obtained on C₁₈ column with the mobile phase of 20 mM pH 3.5 citric acid (H₃Cit)–sodium hydrogen phosphate (Na₂HPO₄) buffer and methanol. Good linearities with correlation coefficients square (R²) greater than 0.998 in the corresponding concentration ranges were observed and the detection limits (S/N = 3) were found in the range from 0.10 to 0.40 nM (l-DOPA: 1.45 nM). The proposed method has been applied to the detection of catecholamines and related compounds in mice liver and brain samples without tedious extraction or purification procedure, which exhibits excellent selectivity and sensitivity in the analysis of complex samples. This work provides an alternative approach in the metabolic research of catecholamines and is helpful for the study of catecholamine metabolism.     

Rough terrain profiling using digital image correlation

Road profiling is an important aspect of vehicle dynamics simulations especially over rough terrains. The accurate measurement of rough terrains allows for more accurate multi body simulations. Three dimensional road profiles are usually performed by utilising a line scan sensor which measures several points lateral to the road. The sensors range from simple road following wheels to LiDAR sensors. The obtained line scans are longitudinally stitched together using the orientation and position of the sensor to obtain a full three dimensional road profile. The sensor’s position and orientation therefore needs to be accurately determined in order to combine the line scans to create an accurate representation of the terrain. The sensor’s position and orientation is normally measured using an expensive inertial measurement unit or Inertial Navigation System (INS) with high sensitivity, low noise and low drift. This paper proposes a road profiling technique which utilises stereography, based on two inexpensive digital cameras, to obtain three-dimensional measurements of the road. The system negates the use of an expensive INS system to determine orientation and position. The data sets also require subsampling which can be computationally expensive. A simple subsampling routine is presented which takes advantage of the structure of the data sets to significantly speed up the process.     

1H-NMR Metabolic Profiling and Antioxidant Activity of Saffron (Crocus sativus) Cultivated in Lebanon

Despite the beneficial health properties shown by Lebanese saffron, its qualitative and quantitative composition has never been investigated before. In the present study, NMR spectroscopy, together with antioxidant activity assays, were applied to evaluate the chemical composition of saffron samples of different geographical origins (Lebanon, Italy, Iran, and India) and to categorize the Lebanese saffron for the first time. The distinction between Lebanese saffron and that produced in other countries was attributed to its higher linolenic and linoleic fatty acids, glucose and picrocrocin contents. Moreover, spices produced in three different regions of the Lebanese territory have been clearly differentiated. Saffron cultivated in the Qaa region displayed a high glucose, fatty acids and polyphenols content, whereas Hermel saffron exhibited the largest rate of picrocrocin and glycosylated carotenoids. Finally, samples from Baalbeck showed lower rates for the majority of metabolites. Moreover, Lebanese saffron showed a high antioxidant activity in ABTS and DPPH assays. A low dose of saffron extract (10 µg/mL) inhibited the growth of human lung adenocarcinoma cells, probably due to the high polyphenolic content. This study highlights the quality and peculiarity of Lebanese saffron cultivated in Northern Beqaa district and allows for a good discrimination between spices produced in relatively close territory.     

Depth profiling of polymer samples using Ga+ and C60+ ion beams

In this contribution, we focus on the use of C₆₀⁺ ions for depth profiling of model synthetic polymers: polystyrene (PS) and poly(methylmethacrylate) (PMMA). These polymers were spin coated on silicon wafers, and the obtained samples were depth‐profiled both with Ga⁺ ions and C₆₀⁺ ions. We observed an important yield enhancement for both polymers when C₆₀⁺ ions are used. More specifically, we discuss here the decrease in damage obtained with C₆₀, which is found to be very sensitive to the nature of the polymer. During the C₆₀⁺ sputtering of the PMMA layer, after an initial decrease, a steady state is observed in the secondary ion yield of characteristic fragments. In contrast, for PS, an exponential decrease is directly observed, leading to an initial disappearance cross section close to the value observed for Ga⁺. Though there is a significant loss of characteristic PS signal when sputtering with C₆₀⁺ ions beams, there are still significant enhancements in sputter yields when employing C₆₀⁺ as compared to Ga⁺. Copyright © 2008 John Wiley & Sons, Ltd.