Development and assessment of scoring functions for protein identification using PMF data

PMF is one of the major methods for protein identification using the MS technology. It is faster and cheaper than MS/MS. Although PMF does not differentiate trypsin-digested peptides of identical mass, which makes it less informative than MS/MS, current computational methods for PMF have the potential to improve its detection accuracy by better use of the information content in PMF spectra. We developed a number of new probability-based scoring functions for PMF protein identification based on the MOWSE algorithm. We considered a detailed distribution of matching masses in a protein database and peak intensity, as well as the likelihood of peptide matches to be close to each other in a protein sequence. Our computational methods are assessed and compared with other methods using PMF data of 52 gel spots of known protein standards. The comparison shows that our new scoring schemes have higher or comparable accuracies for protein identification in comparison to the existing methods. Our software is freely available upon request. The scoring functions can be easily incorporated into other proteomics software packages.     

Physical and chemical properties of bio-oils from microwave pyrolysis of corn stover

This study was aimed to understand the physical and chemical properties of pyrolytic bio-oils produced from microwave pyrolysis of corn stover regarding their potential use as gas turbine and home heating fuels. The ash content, solids content, pH, heating value, minerals, elemental ratio, moisture content, and viscosity of the bio-oils were determined. The water content was approx 15.2 wt%, solids content 0.22 wt%, alkali metal content 12 parts per million, dynamic viscosity 185 mPa.s at 40 degrees C, and gross high heating value 17.5 MJ/kg for a typical bio-oil produced. Our aging tests showed that the viscosity and water content increased and phase separation occurred during the storage at different temperatures. Adding methanol and/or ethanol to the bio-oils reduced the viscosity and slowed down the increase in viscosity and water content during the storage. Blending of methanol or ethanol with the bio-oils may be a simple and cost-effective approach to making the pyrolytic bio-oils into a stable gas turbine or home heating fuels.     

Novel biodegradable poly(1,8-octanediol malate) for annulus fibrosus regeneration

A novel elastic scaffold that simulates the deformability of annulus fibrosus (AF) and has good biocompatibility was developed. The scaffold was formed of a malic acid-based polyester poly(1,8-octanediol malate) (POM), which was synthesized by direct polycondensation. The tensile strength of POM gradually increased with the extension of the polymerization time, while the degradation rate decreased. Rat AF cells proliferated on the POM films and maintained their phenotype. The 3D scaffold also supported the growth of the AF cells, as confirmed by Safranin-O and type II collagen staining. POM also demonstrated a good biocompatibility in an in vivo foreign body response assay, an important prerequisite for tissue engineering applications. This study suggests that elastic POM scaffold may be an ideal candidate for AF tissue engineering.     

Liquid chromatography—tandem mass spectrometry analysis of the DNA adducts of aristolochic acids

Electrophilic attack of aristolactam-nitrenium ion by the C7 position to the exocyclic amino group in the DNA bases led to the formation of the major adducts. In this study, liquid chromatography coupled with electrospray ionization tandem mass spectrometry was applied to the study of DNA adducts of aristolochic acid (AA). When DNA (bases and CT-DNA) was incubated with AA, dG-AAI, dG-AAII, dA-AAI, dA-AAII, dC-AAI, and dC-AAII were detected and characterized. The dC adducts of AA were identified for the first time. The soft ionization technology allowed detection of the intact DNA adducts. High-resolution MS and MS-MS capabilities of a quadrupole time-of-flight mass spectrometer were shown to be efficient for DNA adducts analysis. DNA-AA adducts showed characteristic fragmentation patterns in MS-MS analysis. The dissociative loss of 116 Da from the DNA-AA adducts, which resulted from internal hydrogen transfer and cleavage at the C-N glycosidic bond, provided a characteristic fragment for the structural elucidation.     

Designed synthesis of mesoporous solids via nonionic-surfactant-templating approach

The continual needs for improved performances in applications derived by diversified compositions and mesostructures have pushed forward the development of mesoporous solids. The nonionic-surfactant-templating approach has been a critical route in this advancement. A large number of nonionic surfactants widely used in industries and featured with low cost, low toxicity, bio-degradation and ordered microdomains can be utilized as effective templates to the design and synthesis of abundant mesoporous solids. This feature article provides recent reports on the use of nonionic surfactant self-assembly as examples to fabricate high-quality ordered mesoporous solids which illustrates advances in synthesis and understanding of formation mechanisms. It includes the selection of surfactants, a summary of the effects of synthetic parameters, the current understanding of the synthetic pathways and related mechanisms with some emphasis on evaporation induced self-assembly (EISA), as well as the design and synthesis on the microscale (atomic and molecular compositions) and mesoscale (mesostructures). Preliminary applications of mesoporous solids particularly in optical devices, electrodes and biomaterials are also presented.     

Synthesis and characterization of sol–gel alumina nanofibers

Abstract Alumina nanofibers of high aspect ratio with surface area of >300 m² g⁻¹ has been prepared successfully in bulk quantities by the sol–gel method. The synthesis parameters including the binary water–alcohol solvent system to aluminium isopropoxide ratio, pH, type of solvent and aging temperature affect the uniformity and formation of nanofibers. It is proposed that alumina nanofibers were formed by the curling of the nanosheets upon condensation after the hydrolysis. The phase evolution of alumina nanofibers from pseudoboehmite to α phase has been shown by XRD and FTIR. ²⁷Al NMR investigations show that the Al atoms are six and four coordinated. The morphology of the alumina nanofibers does not change much as the calcination temperature was increased. In addition, the average pore size increases and the BET surface area decreases as a function of calcination temperature. The thermal behavior of alumina nanofibers was investigated by TGA. Graphical Abstract      

Immobilized tris(hydroxymethyl)aminomethane as a scaffold for ion-selective ligands: the auxiliary group effect on metal ion binding at the phosphate ligand

The metal ion affinities of a ligand in a polymer-supported reagent can be enhanced by the presence of a proximate group capable of hydrogen bonding. A new polymer-supported reagent has been synthesized by immobilizing tris(hydroxymethyl)aminomethane (Tris) onto cross-linked poly(vinylbenzyl chloride) and then phosphorylating the -OH moieties. The -NH- acts as the auxiliary group to increase the extent of complexation by the phosphate ligand. Additionally, Tris acts as a scaffold, wherein the phosphate ligands are in a known stereochemical arrangement. The Tris resin is mono-, di-, and triphosphorylated, depending on the concentration of the phosphorylating agent. The highest metal ion affinities are found with the resin having a phosphorus-to-nitrogen ratio of 2.36, consistent with one-third of the ligands being triphosphorylated and the remainder being diphosphorylated. The unphosphorylated Tris and phosphonate diester resins have no ionic affinities under the same conditions. Trivalent ions (Fe(III), Al(III), La(III), Eu(III), Lu(III)) are preferred over divalent ions (Pb(II), Cd(II), Cu(II), Zn(II)) from solutions at pH 2. The distribution coefficients of the divalent ions correlate with the Misono softness parameters, indicating that the polarizability of the phosphoryl oxygen is important to binding of the metal ions. The mechanism of complexation is probed with Fe(III) in 0.01-5 M HNO3 and HCl. The high affinities are ascribed to activation of the P=O ligand toward metal ion binding by the N-H moieties acting as auxiliary groups, coupled with intraligand cooperation among the phosphate moieties at a given site. FTIR spectra show that the P=O band at 1261 cm-1 shifts as a function of the extent of hydrogen bonding. Binding at the P=O requires a balance between activation by hydrogen bonding and availability of the lone pair electrons to the metal ions.     

Microwave assisted volatilization of silicon as fluoride for the trace impurity determination in silicon nitride by dynamic reaction cell inductively coupled plasma-mass spectrometry

A low pressure microwave assisted vapor phase dissolution procedure for silicon nitride and volatilization of in situ generated SiF₄ has been developed using H₂SO₄, HF and HNO₃ for the determination of trace impurities present in silicon nitride. Sample was taken in minimum amount (0.5 mL for 100 mg) of H₂SO₄ and treated with vapors generated from HF and HNO₃ mixture in presence of microwaves in a closed container. An 80 psi pressure with ramp and hold times of 30 min and 60 min respectively, operated twice, resulted in 99.9% volatilization of Si. Matrix free solutions were analyzed for impurities using DRC-ICP-MS. The recoveries of Cr, Mn, Fe, Ni, Co, Cu, Zn, Sr, Y, Cd, Ba and Pb were between 80 and 100% after volatilization of Si. The blanks were in lower ng g⁻¹ with method detection limits in lower ng g⁻¹ to sub ng g⁻¹ range. The method was applied for the analysis of two silicon nitride samples.     

Synthesis, reactivity, and structural characterization of sodium and ytterbium complexes containing new imidazolidine-bridged bis(phenolato) ligands

A new imidazolidine-bridged bis(phenol) [ONNO]H2 ([ONNO]H2=1,4-bis(2-hydroxy-3,5-di-tert-butyl-benzyl)imidazolidine) was prepared in relatively high yield by Mannish reaction of 2,4-di-tert-butylphenol, formaldehyde, and ethylenediamine in a 2:3:1 molar ratio. Reaction of the bis(phenol) with NaH in THF, after workup, afforded the sodium bis(phenolate) {[ONNO]Na2(THF)2}2.2THF (1) as a dimeric tetranuclear complex in an almost quantitative yield. Reaction of YbCl3 with complex 1 in a 2:1 molar ratio in THF, in the presence of HMPA, produced the desired bis(phenolate) ytterbium dichloride as bimetallic complex [ONNO]{YbCl2(HMPA)}2.2.5C7H8 (2). Complex 2 can be used as a precursor for the synthesis of ytterbium derivatives by salt metathesis reactions. Reaction of complex 2 with NaOiPr in a 1:2 molar ratio in THF led to the formation of bimetallic alkoxide [ONNO]{Yb(mu-OiPr)Cl(HMPA)}2.THF (3). However, the residual chlorine atoms in complex 3 are inactive for the further substituted reaction. Further study revealed that the bulkiness of the reagent has profound effect on the outcome of the reaction. Complex 2 reacted with bulky NaOAr (ArO=2,6-di-tert-butyl-4-methylphenoxo) or NaNPh2 in a 1:2 molar ratio under the same reaction conditions, after workup, to give the ligand redistributed products, (ArO)2YbCl(HMPA)2 (4) and [ONNO]YbCl(HMPA)2 (5) for the former and complexes 5 and (Ph2N)2YbCl(HMPA)2 (6) for the latter. If the molar ratio of complex 2 to NaNPh2 decreased to 1:4, the expected ligand redistributed products [ONNO]YbNPh2(HMPA) (7) and (Ph2N)3Yb(HMPA)2.C7H8 (8) can be isolated in high yields. All of the complexes were well characterized, and the definitive molecular structures of complexes 1-4, 7, and 8 were provided by single-crystal X-ray analysis.