Micro- and nano-mechanical characterization of polyamide 11 and its composites containing cellulose nanofibers

Nanocomposites from polyamide 11 and dried cellulose nanofibers (CNs), 16–30 nm in thickness and 50–400 nm in length, were prepared via direct melt mixing and their micro- and nano-mechanical properties were studied. (PF) QNM (Quantitative Nanomechanical Mapping) method was used to map nanomechanical properties at the surface of polyamide 11 and nanocomposites. This new AFM method emphasized both the increased modulus in nanocomposites as compared to the matrix and the microstructure on different levels in polyamide 11 and its nanocomposites. PF QNM showed that their crystalline structure consists of bundles of lamellar stacks, 200–350 nm in width and 20–40 nm wide lamellar stacks. Moreover, PF QNM study emphasized higher structural order in nanocomposites with 3 and 5 wt.% CNs and lower in the nanocomposite with 8 wt.% CNs as compared to the reference. These observations were verified and are consistent with both crystallinity values determined by DSC and micro-mechanical test results. The oriented bundles of lamellar stacks, observed by PF QNM, could be considered as the main blocks determining high mechanical properties for the studied nanomaterials.     

Combination of FASP and fully automated 2D‐LC‐MS/MS allows in‐depth proteomic characterization of mouse zymogen granules

Zymogen granule (ZG) constituents play important roles in pancreatic injury and disease. In previous studies, proteomic analyses with rat zymogen granules were separated by two‐dimensional gel electrophoresis or one‐dimensional SDS–PAGE, followed by in‐gel tryptic digestion. In order to overcome the disadvantage of in‐gel digestion and to carry out further in‐depth proteomic analysis of the zymogen granules, in this study, by combining a filter‐aided sample preparation method and fully automated 2D‐LC‐MS/MS technique, 800 ZG proteins were identified with at least two unique peptides for each protein, 75% of which have not been previously reported. The identified proteins revealed broad diversity in protein identity and function. This is the largest dataset of ZG proteome, and also the first dataset of the mouse ZG proteome, which may help elucidate on the molecular architecture of ZGs and their functions. Copyright © 2012 John Wiley & Sons, Ltd.     

Quantitative leak test for microholes and microtears in whole gloves and glove pieces

The current leak tests for gloves are qualitative. The developed quantitative leak test uses vacuum pressure to draw measured volumes of water to detect microholes/tears in whole gloves and glove pieces. A modified plastic vacuum desiccator interfaced with a Frazier air permeability tester allowed exposure of disposable unsupported/unlined/powderless Kimtech Blue nitrile to 50 mL of water for glove pieces or to 600 mL within a whole glove at vacua of 8–9 in. (20–23 cm) and 11–12 in. (28–30 cm) water gauge, respectively. Punctures of known dimensions were made before testing in specific glove areas using 21-, 22-, 26-, 30-, and 33-gauge needles (outer/inner diameters in micrometres of 873/514, 794/413, 635/311, 476/127, 318/159 and 238/133, respectively). The length of the punctures varied from 0.13 ± 0.01 to 0.80 ± 0.11 mm. Flow rates of water through the holes/tears ranged from 2.5 ± 0.4 to 106 ± 7 mL/min for glove pieces. For whole gloves, the ranges were from 31 ± 9 to 543 ± 110 mL/min in the palm area; and 0.23 ± 0.06 to 82 ± 18 mL/min in the finger/fingertip area. The method quantified tear lengths as short as 0.13 ± 0.01 mm.     

Cyclic sample pooling using two‐dimensional liquid chromatography system enhances coverage in shotgun proteomics

We report a cyclic sample pooling technique devised in two‐dimensional liquid chromatography–electrospray ionization mass spectrometry (LC‐ESI‐MS) shotgun proteomics that renders deeper proteome coverage; we combined low pH reversed‐phase (RP) LC in trifluoroacetic acid in the first dimension, followed by cyclic sample pooling of the eluate and low‐pH RP‐LC in formic acid in the second dimension. The new protocol has a significantly higher resolving power suitable for LC‐ESI‐MS/MS shotgun proteomics. Copyright © 2013 John Wiley & Sons, Ltd.     

Quantitative assessment of rhodamine spectra

With the development of single-molecule detection and super-resolution fluorescence imaging, rhodamine dyes gain new life. Through the modification of the N-substituents and the replacement of the oxygen atom in xanthene, the wavelength and brightness can be effectively changed. However, the spectra of rhodamine, especially due to the balance between ring-closed non-fluorescent lactone and ring-opened fluorescent zwitterion/cation, are sensitive to interference from various environmental factors. In this way, the spectral data of various rhodamines reported by different research groups under different test conditions lacked comparability, sometimes even lacked accuracy. In order to meet the requirements for the accuracy and uniformity of spectral data in the research of single molecule imaging and dye structure-fluorescence relationship study, we have tested the spectra of fifteen rhodamine dyes that cover the visible and near-infrared regions under exactly the same conditions. By studying the dependence of the spectra on dye concentrations, it was confirmed that 1 μmol/L was ideal for detection less from the interference of dye molecule aggregation. We provide comprehensive and reliable spectral data of these fifteen dyes, which are expected to be used as references for future research. And the direct comparison of different rhodamine spectra would help to understand the structure-fluorescence relationship of rhodamines.     

一种面向PX装置成品杂质含量检测的拉曼光谱分析法

面向对二甲苯(PX)成品的在线分析问题,为克服色谱分析法的不足,本文提出了一种基于拉曼光谱的PX成品杂质含量分析方法。为了克服激光中心波长与功率波动带来的不良影响,提出了激光中心波长自动校正与PX特征峰归一化方法;同时,结合相关分析获取了主要杂质的特征波段,并采用偏最小二乘算法进行定量分析。针对11个未知样本,PLS模型对甲苯(MB)、乙苯(EB)、间二甲苯(MX)、邻二甲苯(OX)的标准预测误差分别为0.03%、0.11%、0.02%、0.03%。实验结果表明,拉曼光谱法能够快速、准确且无损地测定PX成品中主要杂质的含量,为在线拉曼分析系统的开发奠定了方法基础。     

In Situ Proteome Profiling and Bioimaging Applications of Small‐Molecule Affinity‐Based Probes Derived From DOT1L Inhibitors

DOT1L is the sole protein methyltransferase that methylates histone H3 on lysine 79 (H3K79), and is a promising drug target against cancers. Small‐molecule inhibitors of DOT1L such as FED1 are potential anti‐cancer agents and useful tools to investigate the biological roles of DOT1L in human diseases. FED1 showed excellent in vitro inhibitory activity against DOT1L, but its cellular effect was relatively poor. In this study, we designed and synthesized photo‐reactive and “clickable” affinity‐based probes (AfBPs), P1 and P2 , which were cell‐permeable and structural mimics of FED1 . The binding and inhibitory effects of these two probes against DOT1L protein were extensively investigated in vitro and in live mammalian cells (in situ). The cellular uptake and sub‐cellular localization properties of the probes were subsequently studied in live‐cell imaging experiments, and our results revealed that, whereas both P1 and P2 readily entered mammalian cells, most of them were not able to reach the cell nucleus where functional DOT1L resides. This offers a plausible explanation for the poor cellular activity of FED1 . Finally with P1 / P2 , large‐scale cell‐based proteome profiling, followed by quantitative LC‐MS/MS, was carried out to identify potential cellular off‐targets of FED1 . Amongst the more than 100 candidate off‐targets identified, NOP2 (a putative ribosomal RNA methyltransferase) was further confirmed to be likely a genuine off‐target of FED1 by preliminary validation experiments including pull‐down/Western blotting (PD/WB) and cellular thermal shift assay (CETSA).     

Origin and Prediction of Highly Specific Bond Cleavage Sites in the Thermal Activation of Intact Protein Ions

Predicting the fragmentation patterns of proteins would be beneficial for the reliable identification of intact proteins by mass spectrometry. However, the ability to accurately make such predictions remains elusive. An approach to predict the specific cleavage sites in whole proteins resulting from collision-induced dissociation by use of an improved electrostatic model for calculating the proton configurations of highly-charged protein ions is reported. Using ubiquitin, cytochrome c, lysozyme and β-lactoglobulin as prototypical proteins, this approach can be used to predict the fragmentation patterns of intact proteins. For sufficiently highly charged proteins, specific cleavages occur near the first low-basicity amino acid residues that are protonated with increasing charge state. Hybrid QM/QM′ (QM=quantum mechanics) and molecular dynamics (MD) simulations and energy-resolved collision-induced dissociation measurements indicated that the barrier to the specific dissociation of the protonated amide backbone bond is significantly lower than competitive charge remote fragmentation. Unlike highly charged peptides, the protons at low-basicity sites in highly charged protein ions can be confined to a limited sequence of low-basicity amino acid residues by electrostatic repulsion, which results in highly specific fragmentation near the site of protonation. This research suggests that the optimal charge states to form specific sequence ions of intact proteins in higher abundances than the use of less specific ion dissociation methods can be predicted a priori.     

The impact of blood on liver metabolite profiling – a combined metabolomic and proteomic approach

Metabolomics has entered the well‐established omic sciences as it is an indispensable information resource to achieve a global picture of biological systems. The aim of the present study was to estimate the influence of blood removal from mice liver as part of sample preparation for metabolomic and proteomic studies. For this purpose, perfused mice liver tissue (i.e. with blood removed) and unperfused mice liver tissue (i.e. containing blood) were compared by two‐dimensional gas chromatography time of flight mass spectrometry (GC × GC‐TOFMS) for the metabolomic part, and by liquid chromatography tandem mass spectrometry (LC‐MS/MS) for the proteomic part. Our data showed significant differences between the unperfused and perfused liver tissue samples. Furthermore, we also observed an overlap of blood and tissue metabolite profiles in our data, suggesting that the perfusion of liver tissue prior to analysis is beneficial for an accurate metabolic profile of this organ. Copyright © 2013 John Wiley & Sons, Ltd.