Covariances Simultaneous Component Analysis: a new method within a framework for modeling covariances

In modern omics research, it is more rule than exception that multiple data sets are collected in a study pertaining to the same biological organism. In such cases, it is worthwhile to analyze all data tables simultaneously to arrive at global information of the biological system. This is the area of data fusion or multi‐set analysis, which is a lively research topic in chemometrics, bioinformatics, and biostatistics. Most methods of analyzing such complex data focus on group means, treatment effects, or time courses. There is also information present in the covariances among variables within a group, because this relates directly to individual differences, heterogeneity of responses, and changes of regulation in the biological system. We present a framework for analyzing covariance matrices and a new method that fits nicely in this framework. This new method is based on combining covariance prototypes using simultaneous components and is, therefore, coined Covariances Simultaneous Component Analysis (COVSCA). We present the framework and our new method in mathematical terms, thereby explaining the (dis)similarities of the methods. Systems biology models based on differential equations illustrate the type of variation generated in real‐life biological systems and how this type of variation can be modeled within the framework and with COVSCA. The method is subsequently applied to two real‐life data sets from human and plant metabolomics studies showing biologically meaningful results. Copyright © 2015 John Wiley & Sons, Ltd.     

A Facile Ester Homologation of Carbonyl Compounds Via Ketene-O,S-Acetals

A usefull extension of the available methods for the conversion of carbonyl compounds into ketene-O,S-acetals^1,2,3 has been found in the Peterson olefination with methoxyphenylthiotrimethylsilyl-methyllithium 1 of aldehydes and ketones. The starting material for this reagent 1 was prepared by reaction of methoxyphenylthio-methyllithium^4,5 with chlorotrimethylsilane at -80°C in THF. Deprotonation of the obtained methoxyphenylthiotrimethylsilyl-methane with n-butyllithium at -80°C in THF gave 1 and subsequent addition of the carbonyl compound at -80°C gave mixtures of Z and E ketene-O,S-acetals 2.     

The Role of 2,6‐Diaminopyridine Ligands in the Isolation of an Unprecedented,Low‐Valent Tin Complex

Stabilization of the central atom in an oxidation state of zero through coordination of neutral ligands is a common bonding motif in transition‐metal chemistry. However, the stabilization of main‐group elements in an oxidation state of zero by neutral ligands is rare. Herein, we report that the transamination reaction of the DAMPY ligand system (DAMPY=2,6‐[ArNH‐CH₂]₂(NC₅H₃) (Ar=C₆H₃‐2,6‐iPr₂)) with Sn[N(SiMe₃)₂]₂ produces the DIMPYSn complex (DIMPY=(2,6‐[ArN?CH]₂(NC₅H₃)) with the Sn atom in a formal oxidation state of zero. This is the first example of a tin compound stabilized in a formal oxidation state of zero by only one donor molecule. Furthermore, three related low‐valent Sn^II complexes, including a [DIMPYSn^IICl]⁺[SnCl₃]^? ion pair, a bisstannylene DAMPY{Sn^II[N(SiMe₃)₂]₂}₂, and the enamine complex MeDIMPYSn^II, were isolated. Experimental results and the conclusions drawn are also supported by theoretical studies at the density functional level of theory and ¹¹⁹Sn Mössbauer spectroscopy.     

Biomimetic Synthesis of Materials for Technology

In a world with ever decreasing natural reserves, researchers are striving to find sustainable methods of producing components for technology. Bioinspired, biokleptic and biomimetic materials can be used to form a wide range of technologically relevant materials under environmentally friendly conditions. Here we investigate a range of biotemplated and bioinspired materials that can be used to develop components for devices, such as optics, photonics, photovoltaics, circuits and data storage.     

Bridging Ligand Length Controls AT Selectivity and Enantioselectivity of Binuclear Ruthenium Threading Intercalators

The slow dissociation of DNA threading intercalators makes them interesting as model compounds in the search for new DNA targeting drugs, as there appears to be a correlation between slow dissociation and biological activity. Thus, it would be of great value to understand the mechanisms controlling threading intercalation, and for this purpose we have investigated how the length of the bridging ligand of binuclear ruthenium threading intercalators affects their DNA binding properties. We have synthesised a new binuclear ruthenium threading intercalator with slower dissociation kinetics from ct‐DNA than has ever been observed for any ruthenium complex with any type of DNA, a property that we attribute to the increased distance between the ruthenium centres of the new complex. By comparison with previously studied ruthenium complexes, we further conclude that elongation of the bridging ligand reduces the sensitivity of the threading interaction to DNA flexibility, resulting in a decreased AT selectivity for the new complex. We also find that the length of the bridging ligand affects the enantioselectivity with increasing preference for the ΔΔ enantiomer as the bridging ligand becomes longer.     

Dibutylsilylene Derivatives of Tartaric Acid

Crystals of the bis(tert‐butyl)silylene (DTBS) derivatives of the tartaric acids were synthesized from D ‐, L ‐, rac‐, and meso‐tartaric acid and DTBS bis(trifluoromethanesulfonate): two polymorphs of Si₂tBu₄(L ‐Tart1,2;3,4H_–4) (L ‐ 1a and L ‐ 1b ), the mirror image of the denser modification (D ‐ 1b ) as well as the racemate ( 2 ), and the meso analogue Si₂tBu₄(meso‐Tart1,3;2,4H_–4) ( 3 ). The structures were determined by single‐crystal X‐ray diffraction. The threo‐configured D ‐ and L ‐ (and rac‐) tartrates were coordinated by two tBu₂Si units forming five‐membered chelate rings, whereas the erythro‐configured meso‐tartrate formed six‐membered chelate rings. The new compounds were analyzed by NMR techniques, including ²⁹Si NMR spectroscopy, and single‐crystal X‐ray crystallography.     

Monitoring bisphenol A and estrogenic chemicals in thermal paper with yeast-based bioreporter assay

Bioluminescent Saccharomyces cerevisiae yeast-based bioreporters were used to monitor bisphenol A and other estrogenic chemicals in thermal paper samples collected mainly from Finland on two occasions in 2010/2011, and 2013. The bisphenol A-targeted (BPA-R) and the human oestrogen receptor (hERα) bioreporters were applied to analyse both non-treated and extracted paper samples. Bisphenol A was readily bioavailable to the yeast bioreporters on the non-treated paper samples without any pre-treatment. Detected concentrations ranged from a detection limit of 9–142 μg/g to over 20 mg/g of bisphenol A equivalents in the thermal papers. Low bisphenol A like activities were detected in many samples, and were considered to be caused by residual bisphenol A or other types of bisphenols, such as bisphenol S. Most of the thermal paper samples were toxic to the yeast bioreporters. The toxicity did not, however, depend on the bisphenol A concentration of the samples. The yeast bioreporters were demonstrated to be a robust and cost-efficient method to monitor thermal paper samples for their bisphenol A content and estrogenicity. Thermal paper was considered as a potential BPA source for both human exposure and environmental emission.