Solution structure determination of oligoureas using methylene spin state selective NMR at 13C natural abundance

Ability of N,N'-linked oligoureas containing proteinogenic side chains to adopt a stable helix conformation in solution has been described recently. NMR as well as circular dichroism (CD) spectroscopies were employed to gain insight into their specific fold. It is herein proposed to extend the structural information available on these peptidomimetics by an advantageous use of a methylene spin state selective NMR experiment. Homodecoupling provided by the pulse scheme made it possible to readily measure conformation-dependent (3)J(HH) constants that are difficult if not impossible to obtain with standard NMR experiments. Adding those couplings to the NMR restraints improved the quality of the structure calculations significantly, as judged by a ca 30% decrease of the root mean square deviation (RMSD) obtained over an ensemble of 20 structures. Moreover, accurate determination of individual (1)J(CH) couplings within each methylene group revealed uniform values throughout the oligourea sequence, with (1)J(CH) systematically slightly larger for the pro-S hydrogen than for the pro-R. As shown in this study, the methylene spin state selective NMR experiment displays a good intrinsic sensitivity and could therefore provide valuable structural information at (13)C natural abundance for peptidomimetic molecules and foldamers bearing diastereotopic methylene protons.     

A dive counting density estimation method for Blainville’s beaked whale (Mesoplodon densirostris) using a bottom-mounted hydrophone field as applied to a Mid-Frequency Active (MFA) sonar operation

We present a passive acoustic method for estimating the density of echolocating cetaceans that dive synchronously, based on isolation of dive starts using a field of distributed bottom-mounted hydrophones. The method assumes that all dive starts of the target species within a defined area are detected, and that independent estimates of dive rate and group size are available. We apply the method to estimate the density of Blainville’s beaked whales (Mesoplodon densirostris) at the Atlantic Undersea Test and Evaluation Center (AUTEC) in the Bahamas during the time of a multi-ship active sonar exercise. Estimated densities for the 65 h before the exercise, 68 h during, 65 h after, and the final 43 h monitored were 16.99 (95% CI 13.47-21.43), 4.76 (3.78-6.00), 8.67 (6.87-10.94), and 24.75 (19.62-31.23) respectively, illustrating a possible avoidance reaction. Results for the 65 h before were compared with those from the click count density estimation algorithm developed by Marques et al. [Marques T, Thomas L, Ward J, DiMarzio N, Tyack P. Estimating cetacean population density using fixed passive acoustic sensors. An example with Blainville’s beaked whales. J Acoust Soc Am 2009;125(4):1982-1994]. The click count-based estimate was 19.23 animals/1000 km² (95% CI 12.69-29.13)—similar (13% higher), but with higher variance (CV 21% for click count method versus 12% for the dive count method). We discuss potential reasons for the differences, and compare the utility of the two methods. For both, obtaining reliable estimates of the factors that scale the measured quantity (dive starts or detected clicks) to density is the key hurdle. Defining the area monitored in the dive count method can also be problematic, particularly if the array is small.     

Quantitative analysis results of CE-1 X-ray fluorescence spectrometer ground base experiment

As the nearest celestial body to the earth, the moon has become a hot spot again in astronomy field recently. The element analysis is a much important subject in many lunar projects. Remote X-ray spectrometry plays an important role in the geochemical exploration of the solar bodies. Because of th equasi-vacuum atmosphere on the moon, which has no absorption of X-ray, the X-ray fluorescence analysis is an effective way to determine the elemental abundance of lunar surface. The CE-1 X-ray fluorescence spectrometer (CE-1/XFS) aims to map the major elemental compositions on the lunar surface. This paper describes a method for quantitative analysis of elemental compositions. A series of ground base experiments are done to examine the capability of XFS. The obtained results, which show a reasonable agreement with the certified values at a 30% uncertainty level for major elements, are presented.     

High‐abundance protein depletion: Comparison of methods for human plasma biomarker discovery

Affinity depletion of abundant proteins from human plasma has become a routine sample preparation strategy in proteomics used prior to protein identification and quantitation. To date, there have been limited published studies comparing the performance of commercially available depletion products. We conducted a thorough evaluation of six depletion columns using 2‐DE combined with sophisticated image analysis software, examining the following criteria: (i) efficiency of high‐abundance protein depletion, (ii) non‐specific removal of other than the targeted proteins and (iii) total number of protein spots detected on the gels following depletion. From all the products investigated, the Seppro IgY system provided the best results. It displayed the greatest number of protein spots on the depleted plasma gels, minimal non‐specific binding and high efficiency of abundant protein removal. Nevertheless, the increase in the number of detected spots compared with the second best performing and cheaper multiple affinity removal column (MARC) was not shown to be statistically significant. The ProteoPrep spin column, considered to be the “deepest” depletion technique available at the time of conducting the study, surprisingly displayed significantly fewer spots on the flow‐through fraction gels compared with both the Seppro and the MARC. The spin column format and low plasma capacity were also found to be impractical for 2‐DE. To conclude, we succeeded in providing an overview of the depletion columns performances with regard to the three examined areas. Our study will serve as a reference to other scientists when deciding on the optimal product for their particular projects.     

Differentiation of Four Pairs of Isomers by Comparing Their Relative Abundances of Fragment Ions

Based on the LC-ESI/MSn technique, the four pairs of isomers of psoralen and isopsoralen, imperatorin and isoimperatorin, neohesperidin and hesperidin, naringin and narirutin were distinguished mainly by comparison of the relative abundances of their major fragment ions. Because of the effect of the hydrogen on the C8 of psoralen, the intensity of the fragment ion formed by the loss of CO2 was relatively increased. By comparing the abundance of the product ions formed by the loss of CO and 2CO, the isomers ...     

Quantitative Proteomics and Differential Protein Abundance Analysis after Depletion of Putative mRNA Receptors in the ER Membrane of Human Cells Identifies Novel Aspects of mRNA Targeting to the ER

In human cells, one-third of all polypeptides enter the secretory pathway at the endoplasmic reticulum (ER). The specificity and efficiency of this process are guaranteed by targeting of mRNAs and/or polypeptides to the ER membrane. Cytosolic SRP and its receptor in the ER membrane facilitate the cotranslational targeting of most ribosome-nascent precursor polypeptide chain (RNC) complexes together with the respective mRNAs to the Sec61 complex in the ER membrane. Alternatively, fully synthesized precursor polypeptides are targeted to the ER membrane post-translationally by either the TRC, SND, or PEX19/3 pathway. Furthermore, there is targeting of mRNAs to the ER membrane, which does not involve SRP but involves mRNA- or RNC-binding proteins on the ER surface, such as RRBP1 or KTN1. Traditionally, the targeting reactions were studied in cell-free or cellular assays, which focus on a single precursor polypeptide and allow the conclusion of whether a certain precursor can use a certain pathway. Recently, cellular approaches such as proximity-based ribosome profiling or quantitative proteomics were employed to address the question of which precursors use certain pathways under physiological conditions. Here, we combined siRNA-mediated depletion of putative mRNA receptors in HeLa cells with label-free quantitative proteomics and differential protein abundance analysis to characterize RRBP1- or KTN1-involving precursors and to identify possible genetic interactions between the various targeting pathways. Furthermore, we discuss the possible implications on the so-called TIGER domains and critically discuss the pros and cons of this experimental approach.     

Synthesis and characterization of peroxo complexes of uranium(VI) with aroylhydrazone ligands

The uranium(VI) peroxo complexes containing aroylhydrazones ligands having composition [UO(O₂)L-L(NO₃)₂]·H₂O (where L-L = Benzoic acid[1-(Furan-2-yl)methylene] hydrazide, Benzoic acid[(thiophene-2-yl)methylene] hydrazide, Benzoic acid[1-(thiophene-2-yl)ethylidene] hydrazide, Benzoic acid(phenylmethylene) hydrazide, Benzoic acid[1-(anisol-3-yl)methylene] hydrazide and Benzoic acid[(p-chlorobenzyl)methylene] hydrazide are reported. The complexes were characterized by various physico-chemical techniques, viz. elemental analysis, molar conductivity, magnetic susceptibility measurements, infra red, electronic, mass spectral and TGA/DTA studies. These studies revealed that complexes are non-electrolytes and diamagnetic in nature. The ligands are bound to metal in a bidentate mode. Thermal analysis results provide conclusive evidence for the presence of water molecules in the complexes. Mass spectra confirm the molecular mass of the complexes. Antifungal activity of complexes revealed enhanced activity of complexes as compared to the corresponding ligands.     

Proteomic characterization of human platelet-derived microparticles

Microparticles (MPs) are small fragments of apoptotic or activated cells that may contribute to pathological processes in many diseases. Platelet-derived MPs (PMPs) are the most abundant type of MPs in human blood. To characterize the proteins in PMPs we used a shotgun proteomics approach by nanoHPLC separation followed by MS analysis on an LTQ Orbitrap XL. PMPs were produced from isolated platelets stimulated with adenosine diphosphate (ADP). We developed an analytical platform constituted by two different steps: in the first one we used a standard shotgun strategy; in the second one, to improve low-molecular weight, low-abundance-proteins identification, the samples were fractionated using hydrogel nanoparticles, an enrichment system based on a mixed mechanism of dimensional exclusion and colorant affinity. This was chosen to tackle a common issue with shotgun approaches, in which the low-abundance proteins are not detected when surveys are on a broad scale. By means of the entire analytical platform, we identified 603 proteins, 243 of which were not previously identified. A simple and straightforward procedure for the study of PMPs was provided, producing a tool for further understanding their biological and pathological roles, and a baseline for future studies aimed at discovering biomarkers involved in several diseases.     

共振粒子的化学势和粒密度、能密度

研究了相对论重离子碰撞中产生的共振物质的统计性质，讨论了共振粒子的化学势和净粒子密度的关系. 计算了总粒子密度和能量密度，研究和分析了他们和净粒子密度的关系，并估算了总粒子密度相对于正常核密度(0.16fm－3)的倍数；在RHIC能量约为5-8倍，在SPS能量约为3-6倍. 还研究了各种粒子成分随温度的变化，揭示出几个温度区间段对应AGS、SPS和RHIC三个能区，各区间中主要粒子成分分别为重子、奇异子和介子.