A Survey of Orbitrap All Ion Fragmentation Analysis Assessed by an R MetaboList Package to Study Small-Molecule Metabolites

Leukemia cell and melanoma tumor tissue extracts were studied for small (mostly m/z?<?250) polar metabolites by LC-ESI-HRMSⁿ analysis powered by a hybrid Quadrupole-Orbitrap. MS data were simultaneously acquired in fast polarity switching mode operating in MS¹ and MS/MS (All Ion Fragmentation, AIF) full-scan analyses at high mass resolution. Positive metabolite assignments were achieved by AIF analysis considering at least two characteristic transitions. Targeted metabolite profiling was achieved by the relative quantification of 18 metabolites through spiking of their respective deuterated counterparts. Manual data processing of MS¹ and AIF scans were compared for the accurate determination of natural metabolites and their deuterated analogs by chromatographic alignment and peak area integration. Evaluation of manual and automated (MetaboList R package) AIF data processing yielded comparable results. The versatility of AIF analysis also enabled the untargeted metabolite profiling of leukemia and melanoma samples in which 22 and 53 compounds were, respectively, identified outside those studied by labeling. The main limitation of this method was that low abundance metabolites with scan rates below 8 scans/peak could not be accurately quantified by AIF analysis. The combination of AIF analysis with MetaboList R package represents an opportunity to move towards automated, faster, and more global metabolomics approaches supported by an entirely flexible open source data processing platform freely available from Comprehensive R Archive Network (CRAN, https://CRAN.R-project.org/package=MetaboList).     

Immobilization of Tyrosinase on Chitosan — An Optimal Approach to Enhance the Productivity of L‐DOPA from L‐Tyrosine

Tyrosinase was immobilized on Chitosan (CTS) beads to produce 3,4‐dihydroxy‐L‐phenylalanine (L ‐DOPA) from L ‐tyrosine. Epichlorohydrin (ECH), ethylene glycol diglycidyl ether (EGDE), and glutaraldehyde (GLU) were used as coupling agents, respectively. Ultraviolet/visible measurements on CTS films showed that the reaction intermediate (L ‐dopaquinone) attacked the amino groups on CTS, so the amine residues on chitosan were capped by acetic acid anhydride (Ac) or formaldehyde (Fm) to avoid the deactivation of the immobilized tyrosinase. The pH and temperature of the maximal rate to produce L‐DOPA were investigated. GLU (coupling agent) and Ac (capping agent) were selected for practical utility. A 7.5% (w/v) concentration of GLU was found to attain maximal activity of the immobilized enzyme. The thermal stability of tyrosinase immobilized on CTS‐GLU‐Ac, and after treatment with sodium borohydride, was enhanced to a great extent. The L ‐DOPA converting efficiency in the environmental conditions of this study decreased from 45.1% to 39.9% (between 1^st and 30^th batch). This immobilized tyrosinase can be used practically in the production of L‐DOPA from L‐tyrosine.     

Temperature dependence of charge recombination in Heliobacillus mobilis

Transient absorption difference spectroscopy was used to study the temperature dependence of the P798+ decay kinetics in heliobacteria. For membrane samples, two components were obtained from the fitting of kinetic traces in the temperature range of 4-29 degrees C. A 3-9 ms component representing the cytochrome (cyt) c oxidation has an activation energy of 33.0 +/- 2.8 kJ/mol. A 12-22 ms component representing either P798+FX- or P798+FA/B- recombination has an activation energy of 15.3 +/- 2.4 kJ/mol. In isolated reaction centers (RC), only one 14 ms component due to P798+FX- recombination was obtained in this temperature range. The Arrhenius plot shows that the recombination rate of this P798+FX- state is temperature independent in the near room temperature range. For RC in the temperature range of 60-298 K, a 12-15 ms decay was obtained at temperatures greater than 240 K. Biphasic decay traces (12-15 ms and 2-4 ms components) were obtained at temperatures between 170 K and 230 K. Only one 2-4 ms component was found at temperatures lower than 160 K. The gradual switchover from the 12-15 ms to the 2-4 ms component upon cooling may indicate the shift of the P798+FX- recombination state to a state that is prior to P798+FX-, although other interpretations can not be excluded. The absorption difference spectrum (delta A @ 160 K - delta A @ 240 K) in the blue region shows a positive amplitude below 405 nm and a negative amplitude above 405 nm implying that the 2-4 ms decay component may be due to the recombination of P798+A1-, where A1 is a quinone-type acceptor.     

Kinetics and Mechanisms of Acetylcholinesterase and Butyrylcholinesterase Inhibition by Cardiovascular Drugs and Benzodiazepines

The goal of this work is to determine enzyme kinetics and mechanisms of acetylcholinesterase and butyrylcholinesterase inhibition by five cardiovascular drugs, lovastatin, simvastatin, amlodipine besylate, nifedipine, and hydralazine hydrochloride, and two benzodiazepines, diazepam and chlordiazepoxide hydrochloride. All drugs in this study are reversible mixed‐type inhibitors of acetylcholinesterase and butyrylcholinesterase. The pK_i values for acetylcholinesterase and butyrylcholinesterase inhibition by the cardiovascular drugs are linearly correlated with the molecular weights of the drugs with the slopes of 0.005 and 0.0021, respectively. Therefore, van der Waals' interactions between acetylcholinesterase and the cardiovascular drugs are stronger than those between butyrylcholinesterase and the drugs. This is probably due to a smaller active site gorge and a more significant peripheral anionic substrate binding site of acetylcholinesterase than those of butyrylcholinesterase. The fact that the pK_i values for both butyrylcholinesterase and acetylcholinesterase inhibition by the cardiovascular drugs are linearly correlated with each other suggests that both enzyme inhibition reactions proceed via a common mechanism. Furthermore, amlodipine besylate may be useful in Alzheimer's disease treatment similar to donepezil.     

Interrupted Fischer Indolization Approach toward the Communesin Alkaloids and Perophoramidine

A concise approach toward the total synthesis of the communesin alkaloids and perophoramidine is reported. The strategy relies on the use of the interrupted Fischer indolization to build the tetracyclic indoline core of the natural products. Studies to probe the scope and limitations of this plan are presented. Although the methodology does not tolerate a C8-allyl substituent en route to the challenging vicinal quaternary stereocenters, variation at C7 and on the C ring is permitted.     

Time-resolved spectroscopy of energy transfer and trapping upon selective excitation in membranes of Heliobacillus mobilis at low temperature

Transient absorption difference spectra in the Qy absorption band of bacteriochlorophyll (BChl) g and in the 670 nm absorption band of the primary acceptor A0 in membranes of Heliobacillus mobilis (Hc. mobilis) were measured at 20 K upon selective excitation at 668, 793, 810, and 815 nm with a 5 nm spectral bandwidth. When excited at 793 nm, the spectral equilibration of excitations from shorter to longer wavelength-absorbing pigments occurred within 3 ps and mostly localized at the band centered around 808 nm. When excited at 668 nm, the excitation energy transfer from the 670 nm absorbing pigment to the Qy band of BChl g took less than 0.5 ps, and the energy redistribution occurred and localized at 808 nm as in the case of the 793 nm excitation. All of the excitations were localized at the long wavelength pigment pool centered around 810 or 813 nm when excited at 810 or 815 nm. A slower energy transfer process with a time constant of 15 ps was also observed within the pool of long wavelength-absorbing pigments upon selective excitation at different wavelengths as has been observed by Lin et al. (Biophys. J. 1994, 67, 2479) when excited at 590 nm. Energy transfer from long wavelength antenna molecules to the primary electron donor P798 followed by the formation of P+ took place with a time constant of 55-70 ps for all excitations. Direct excitation of the primary electron acceptor A0, which absorbed at 670 nm, showed the same kinetic behavior as in the case when different forms of antenna pigments were excited in the Qy region. This observation generally supports the trapping-limited case of energy transfer in which the excitations have high escape probability from the reaction center (RC) until the charge separation takes place. Possible mechanisms to account for the apparent "uphill" energy transfer from the long wavelength antenna pigments to P798 are discussed.     

From Chemistry to Translational Medicine: The Application of Proteomics to Cancer Biomarker Discovery and Diagnosis

The study of complex protein mixtures and their interactions in cells and tissues has been difficult due to the tedious process involved in their characterization and analysis. The recent emergence of fast‐evolving and state‐of‐the‐art proteomics methodologies has provided a rapid and scalable platform for understanding the comprehensive proteome profiles from complex whole tissues or cells of various biological sources. Therefore, proteomics has been increasingly valuable to examine real‐time changes in protein expression of various tissues or body fluids from patients with various diseases, especially cancer, resulting in the identification of clinically useful biomarkers for diagnosis, prognosis and disease staging. In this review, we focus on potential biomarkers for (1) Helicobacter pylori‐associated gastric cancer, (2) hepatocellular carcinoma (HCC), and (3) renal cell carcinoma (RCC). In addition to the conventional gel‐based proteomics (1‐D or 2‐D gels), we have utilized a more advanced proteomic approach by incorporating stable isotope dimethyl labelling and shotgun proteomics strategy in combination with nanoliquid chromatography and tandem mass spectrometry (nanoLC‐MS/MS) to better characterize the biomarkers in several cancer tissues. By establishing a high‐throughput proteomics platform based on multiple reaction monitoring (MRM), we have successfully detected and analyzed potential protein markers at low concentrations in various normal and tumor tissues. This platform not only highlights the utility of proteomics for biomarker discovery but also can be uniquely applied to disease‐oriented translational medicine for diagnosis of diverse types of cancers and other diseases.     

Cellular automaton simulations for mixed traffic with erratic motorcycles’ behaviours

Modeling mixed traffic composed of motorcycles can be a challenging issue because many erratic motorcyclists may not follow the lane disciplines, particularly when traffic is congested. Based upon the refined cellular automaton (CA) model recently developed by the authors [L.W. Lan, Y.C. Chiou, Z.S. Lin, C.C. Hsu, Physica A 388 (2009) 3917-3930], this paper further proposed a sophisticated CA model to elucidate the erratic motorcycle behaviours in mixed traffic contexts. In addition to the conventional moving forward and lane-change rules, the sophisticated CA model also explicated the lateral drift behaviour for cars moving in the same lane, the lateral drift behaviour for motorcycles breaking into two moving cars, and the transverse crossing behaviour for motorcycles through the gap between two stationary cars in the same lane. Fundamental diagrams and space-time trajectories for vehicles with various car-motorcycle mixed ratios are demonstrated.     

Staged Development of Modified Silicon Dioxide Films

The hydrolytic generation of SiO₂ films from chlorosilanes or alkoxysilanes is interrupted by incorporating labile organic groups which stop SiO₂ formation at a processable prepolymer stage. The monomers for the prepolymer have electron withdrawing substituents in the -position. The organic groups are removed from the prepolymer at low temperature, extruding ethylene. The formation of SiO₂ proceeds by intramolecular condensation of the electronegative substituents which are now in a hydrolytically unstable bond with silicon and hydroxyl groups or ambient moisture. Films of the prepolymer spun onto silicon wafers are converted into uniform SiO₂-rich films at temperatures between 150–400°C.