Comprehensive analysis of microRNA-mRNA co-expression in circadian rhythm

To investigate the potential role of microRNA (miRNA) in the regulation of circadian rhythm, we performed microarray-based expression profiling study of both miRNA and mRNA in mouse liver for 48 h at 4-hour intervals. Circadian miRNA-mRNA target pair is defined as the pair both elements of which show circadian expression patterns and the sequence-based target relationship of which can be predicted. Circadian initiators, Clock and Bmal1, showed inversely correlated circadian expression patterns against their corresponding miRNAs, miR-181d and miR-191, targeting them. In contrast, circadian suppressors, Per, Cry, CKIe and Rev-erba, exhibited positively correlated circadian expression patterns to their corresponding miRNAs. Genomic location analysis revealed that intronic region showed higher abundance of cyclic than non-cyclic miRNAs targeting circadian genes while other (i.e., 3''-UTR, exon and intergenic) regions showed no difference. It is suggested that miRNAs are involved in the regulation of peripheral circadian rhythm in mouse liver by modulating Clock:Bmal1 complex. Identifying specific miRNAs and their targets that are critically involved in circadian rhythm will provide a better understanding of the regulation of circadian-clock system.     

Parameter selection for peak alignment in chromatographic sample profiling: objective quality indicators and use of control samples

In chromatographic profiling applications, peak alignment is often essential as most chromatographic systems exhibit small peak shifts over time. When using currently available alignment algorithms, there are several parameters that determine the outcome of the alignment process. Selecting the optimum set of parameters, however, is not straightforward, and the quality of an alignment result is at least partly determined by subjective decisions. Here, we demonstrate a new strategy to objectively determine the quality of an alignment result. This strategy makes use of a set of control samples that are analysed both spiked and non-spiked. With this set, not only the system and the method can be checked but also the quality of the peak alignment can be evaluated. The developed strategy was tested on a representative metabolomics data set using three software packages, namely Markerlynx™, MZmine and MetAlign. The results indicate that the method was able to assess and define the quality of an alignment process without any subjective interference of the analyst, making the method a valuable contribution to the data handling process of chromatography-based metabolomics data.     

A solution to the 1D NMR alignment problem using an extended generalized fuzzy Hough transform and mode support

This paper approaches the problem of intersample peak correspondence in the context of later applying statistical data analysis techniques to 1D ¹H-nuclear magnetic resonance (NMR) data. Any data analysis methodology will fail to produce meaningful results if the analyzed data table is not synchronized, i.e., each analyzed variable frequency (Hz) does not originate from the same chemical source throughout the entire dataset. This is typically the case when dealing with NMR data from biological samples. In this paper, we present a new state of the art for solving this problem using the generalized fuzzy Hough transform (GFHT). This paper describes significant improvements since the method was introduced for NMR datasets of plasma in Csenki et al. (Anal Bioanal Chem 389:875-885, 15) and is now capable of synchronizing peaks from more complex datasets such as urine as well as plasma data. We present a novel way of globally modeling peak shifts using principal component analysis, a new algorithm for calculating the transform and an effective peak detection algorithm. The algorithm is applied to two real metabonomic ¹H-NMR datasets and the properties of the method are compared to bucketing. We implicitly prove that GFHT establishes the objectively true correspondence. Desirable features of the GFHT are: (1) intersample peak correspondence even if peaks change order on the frequency axis and (2) the method is symmetric with respect to the samples. Figure From chaos to order: heatmaps of a H-NMR spectral segment prior and post sorting on one peak position. Post sorting sample order reveals that peak positions exhibits distinctive patterns which are modeled by the GFHT to establish correspondence. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

高压射频等离子体增强化学气相沉积制备高效率硅薄膜电池的若干关键问题研究

报道了采用高压射频等离子体增强化学气相沉积(RF-PECVD) 制备高效率单结微晶硅电池和非晶硅/微晶硅叠层电池时几个关键问题的研究结果, 主要包括: 1)器件质量级本征微晶硅材料工艺窗口的确定及其结构和光电性能表征; 2)孵化层的形成机理以及减小孵化层的有效方法; 3)氢稀释调制技术对本征层晶化率分布及其对提高电池性能的作用; 4)高电导、高晶化率的微晶硅p型窗口层材料的获得, 及其对减小微晶硅电池p/i界面孵化层厚度和提高电池性能的作用等. 在解决上述问题的基础上, 采用高压RF-PECVD制备的单结微晶硅电池效率达8.16%, 非晶硅/微晶硅叠层电池效率11.61%.     

Investigation of an Allosteric Deoxyhypusine Synthase Inhibitor in P. falciparum

The treatment of a variety of protozoal infections, in particular those causing disabling human diseases, is still hampered by a lack of drugs or increasing resistance to registered drugs. However, in recent years, remarkable progress has been achieved to combat neglected tropical diseases by sequencing the parasites’ genomes or the validation of new targets in the parasites by novel genetic manipulation techniques, leading to loss of function. The novel amino acid hypusine is a posttranslational modification (PTM) that occurs in eukaryotic initiation factor 5A (EIF5A) at a specific lysine residue. This modification occurs by two steps catalyzed by deoxyhypusine synthase (dhs) and deoxyhypusine hydroxylase (DOHH) enzymes. dhs from Plasmodium has been validated as a druggable target by small molecules and reverse genetics. Recently, the synthesis of a series of human dhs inhibitors led to 6-bromo-N-(1H-indol-4yl)-1-benzothiophene-2-carboxamide, a potent allosteric inhibitor with an IC₅₀ value of 0.062 µM. We investigated this allosteric dhs inhibitor in Plasmodium. In vitro P. falciparum growth assays showed weak inhibition activity, with IC₅₀ values of 46.1 µM for the Dd2 strain and 51.5 µM for the 3D7 strain, respectively. The antimalarial activity could not be attributed to the targeting of the Pfdhs gene, as shown by chemogenomic profiling with transgenically modified P. falciparum lines. Moreover, in dose-dependent enzymatic assays with purified recombinant P. falciparum dhs protein, only 45% inhibition was observed at an inhibitor dose of 0.4 µM. These data are in agreement with a homology-modeled Pfdhs, suggesting significant structural differences in the allosteric site between the human and parasite enzymes. Virtual screening of the allosteric database identified candidate ligand binding to novel binding pockets identified in P. falciparum dhs, which might foster the development of parasite-specific inhibitors.     

Systematically Exploring the Chemical Ingredients and Absorbed Constituents of Polygonum capitatum in Hyperuricemia Rat Plasma Using UHPLC-Q-Orbitrap HRMS

Polygonum capitatum as an ethnic medicine has been used to treat urinary tract infections, pyelonephritis and urinary calculi. In our previous study, P. capitatum was found to have anti-hyperuricemia effects. Nevertheless, the active constituents of P. capitatum for treating hyperuricemia were still unclear. In this study, an ultra-high-performance liquid chromatography coupled to quadrupole/orbitrap high-resolution mass spectrometry (UHPLC-Q-Orbitrap HRMS) was used to comprehensively detect the chemical ingredients of P. capitatum and its absorbed constituents in the plasma of hyperuricemia rats for the first time. Xcalibur 3.0 and Compound Discoverer 2.0 software coupled to mzCloud and ChemSpider databases were utilized for qualitative analysis. A total of 114 chemical components including phenolics, flavonoids, tannins, phenylpropanoids, amino acids, amides and others were identified or tentatively characterized based on the exact mass, retention time and structural information. Compared to the previous P. capitatum study, an additional 66 different components were detected. Moreover, 68 related xenobiotics including 16 prototype components and 52 metabolites were found in the plasma of hyperuricemia rats. The metabolic pathways included ring fission, hydrolysis, decarboxylation, dehydroxylation, methylation, glucuronidation and sulfation. This work may provide important information for further investigation on the active constituents of P. capitatum and their action mechanisms for anti-hyperuricemia effects.     

Chemical profiling and quantification analysis of flavonoids in different varieties of Euryales Semen by ultra-high-performance liquid chromatography with tandem mass spectrometry

Euryales Semen was a traditional Chinese medicine, which has been commonly used to treat spermatorrhea, enuresis, and frequent urination. Flavonoids were a critical ingredient in determining the function and quality of Euryales Semen. At present, no effective method has been established for the qualitative of Euryales Semen flavonoids. In this study, an ultra-high-performance liquid chromatography-quadrupole-time of flight-mass spectrometry method was established for flavonoids. By comparison with standard or literature data, 32 flavonoid compounds have been identified in Euryales Semen. Based on the qualitative results, an ultra-high-performance liquid chromatography-triple quadrupole tandem mass spectroscopy method was developed for the main components, and the linearity, the limit of detection, limit of quantification, repeatability, precision, stability, and recovery of the method were verified. The principal component analysis and the hierarchical clustering heatmaps analysis showed that the 30 batches of samples were distinctly separated into the North Gordon Euryale and South Gordon Euryale, and the measured contents of the six flavonoids in North Gordon Euryale were more abundant than in South Gordon Euryale, especially isoquercitrin, hesperetin, and quercetin. It provided a scientific basis for the quality control of Euryales Semen and a theoretical basis for the rational utilization of Euryales Semen resources.     

Ganglioside analysis in body fluids by liquid-phase separation techniques hyphenated to mass spectrometry

The expression of gangliosides in central nervous system is a few times higher than in the extraneural tissue, a characteristic highlighting their major role at this level. Although in very low amounts, gangliosides are ubiquitously distributed in body fluids too, where, depending on many factors, including pathological states, their composition fluctuates, thus having diagnostic value. Ganglioside investigation in biological fluids, which, except for cerebrospinal fluid (CSF), may be sampled noninvasively, was for years impeded by the limited sensitivity of the analytical instrumentation available in glycomics. However, because the last decade has witnessed significant developments in biological mass spectrometry (MS) and the hyphenated separation techniques, marked by a major increase in sensitivity, reproducibility, and data reliability, ganglioside research started to be focused on biofluid analysis by separation techniques coupled to MS. In this context, our review presents the achievements in this emerging field of gangliosidomics, with a particular emphasis on modern liquid chromatography (LC), thin-layer chromatography, hydrophilic interaction LC, and ion mobility separation coupled to high-performance MS, as well as the results generated by these systems and allied experimental procedures in profiling and structural analysis of gangliosides in healthy or diseased body fluids, such as CSF, plasma/serum, and milk.     

A novel double-sampled square-wave voltammetric technique combined with quadruple-disk metallic-glassy carbon electronic tongue for isotonic beverages profiling

This work demonstrates that quadruple-disk electrodes with an innovative design, iridium-platinum, platinum-glassy carbon, and iridium-glassy carbon can effectively function as a single sensor and act as a voltammetric electronic tongue in food profiling. The key strategy used was a novel technique called double-sampled differential square-wave voltammetry (DSSWV), which increased the resolution and enabled extraction of the full, hidden information available in the measuring signals. Four clustering validity indices, namely the Calinski – Harabasz index, Davies – Bouldin index, Silhouette index and gap statistics were employed to select the optimal sensor and methodology for interpreting the current samples. The best expected results were obtained using an iridium-platinum electrode combined with overall cathodic potential modulation using the DSSWV technique. Principal component analysis and polar dendrogram confirmed the correct clustering of different isotonic beverages. However, it was also demonstrated that in some variants of measurement and signal interpretation, it was not possible to group the samples appropriately.     

Highly sensitive liquid chromatographic method combined with online ion suppression to remove interfering anions and mass spectrometry for impurity profiling of paromomycin sulfate

A previously developed high-performance liquid chromatography method combined with pulsed amperometric detection allowed to separate many impurities of paromomycin. However, due to the presence of ion pairing agents and sodium hydroxide in the mobile phase, direct coupling to mass spectrometry for the identification of the chemical structures of the impurities was not an option. Indeed, ion suppression was encountered by trifluoroacetic acid and pentafluoroproponic acid in the mobile phase. A cation self-regenerating suppressor, which was originally designed for increasing analyte conductivity of ammonia and amines analysis in ion chromatography, was coupled between the liquid chromatography and ion trap-time of flight-mass spectrometry and almost all trifluoroacetic acid and pentafluoroproponic acid in the mobile phase was removed. The limit of detection of paromomycin in this integrated system improved significantly to 20 ng/ml (0.4 ng). The chemical structures of 19 impurities were elucidated and seven impurities were reported for the first time.