Logging by Year
Natural Products Log
Logging of recent articles with relevance to our areas of research or of general interest to the field and worthwhile reading; with DOI links to the original publications (copyrighted by the respective publishers).
9/8/2014: Extraction method changes the composition and behavior of oligomeric polyphenols. The quest for the anti-adhesive constituents in cranberries continues - if they would only crystallize, like catechin.
Feliciano RP, Meudt JJ, Shanmuganayagam D, Metzger BT, Krueger CG, Reed JD
Supercritical Fluid Extraction (SFE) of Cranberries Does Not Extract Oligomeric Proanthocyanidins (PAC) but Does Alter the Chromatography and Bioactivity of PAC Fractions Extracted from SFE Residues
Journal of Agricultural and Food Chemistry 62: 7730-7737 (2014)
Abstract: Supercritical fluid extraction (SFE) removed lipophilic compounds and low molecular weight flavonoids from
cranberries. However, SFE did not extract proanthocyanidins (PAC). The SFE PAC-enriched residue was submitted to
fractionation on Sephadex LH-20 using ethanol, ethanol/methanol, and 80% acetone. PAC degree of polymerization (DP) and
ratios of “A-type” to “B-type” interflavan bonds were compared with those of PAC fractions without SFE. Mass spectrometry
showed that when SFE was used, PAC distribution was shifted toward higher DP and contained higher amounts of two and three “A-type” bonds compared to PAC fractions without SFE. The 80% acetone fraction with SFE had significantly greater
extraintestinal pathogenic Escherichia coli (ExPEC) agglutination and significantly lower ExPEC invasion of enterocytes than the
fraction without SFE. Cranberry PAC with higher numbers of “A-type” interflavan bonds are more bioactive in agglutinating
ExPEC and inhibiting ExPEC enterocyte invasion.
9/1/2014: Showing the presence of Ionic Liquids (ILs) in nature: the Ants' solution of a lipophilic alkaloid
Chen L, Mullen GE, Le Roch M, Cassity CG, Gouault N, Fadamiro HY, Barletta RE, O'Brien RA, Sykora RE, Stenson AC, West KN, Horne HE, Hendrich JM, Xiang KR, Davis JH
On the Formation of a Protic Ionic Liquid in Nature
Angewandte Chemie International Edition: in press (2014)
Abstract: The practical utility of ionic liquids (ILs) makes the absence (heretofore) of reported examples from nature quite puzzling, given the facility with which nature produces many other types of exotic but utilitarian substances. In that vein, we report here the identification and characterization of a naturally occurring protic IL. It can be formed during confrontations between the ants S. invicta and N. fulva. After being sprayed with alkaloid-based S. invicta venom, N. fulva detoxifies by grooming with its own venom, formic acid. The mixture is a viscous liquid manifestly different from either of the constituents. Further, we find that the change results as a consequence of formic acid protonation of the N centers of the S. invicta venom alkaloids. The resulting mixed-cation ammonium formate milieu has properties consistent with its classification as a protic IL.
7/31/2014: Fast 2D NMR using ultrafast (UF) and non-uniform sampling (NUS) provide more sensitivity per time to advance metabolomics. How about structure elucidation? How much time does it take to make a good tasting dumpling?
Guennec AL, Giraudeau P, Caldarelli S
Evaluation of Fast 2D NMR for Metabolomics
Analytical Chemistry 86: 5946-5954 (2014)
Abstract: Two-dimensional nuclear magnetic resonance (2D NMR) is increasingly explored as a tool for metabolomics because of its superior resolution compared to one-dimensional NMR (1D NMR). However, 2D NMR is characterized by longer acquisition times, which makes it less suitable for high-throughput studies. In this Article, we evaluated two methods for the acceleration of nD NMR, ultrafast (UF) and nonuniform sampling (NUS), in the context of metabolomics. To this end, model samples mimicking the metabolic profile variations in serum from subjects affected by colorectal cancer and controls were analyzed by 1D 1H NMR along with conventional and accelerated DQF-COSY and HSQC. A statistical analysis (OPLS-DA) yielded similar results for the group separation with all techniques, but biomarker identification from 2D spectra was substantially enhanced, both in terms of number of molecules and easiness of assignment. Most interestingly, fast 2D NMR techniques lead to similar results as conventional 2D NMR, opening the way for high-throughput metabolomics studies using 2D NMR.
7/30/2014: Green is the grass: about error bars, standard deviation, standard error, confidence interval, etc.
Cumming G, Fidler F, Vaux DL
Error bars in experimental biology
J Cell Biol 177: 7-11 (2007)
Abstract: Error bars commonly appear in figures in publications, but experimental
biologists are often unsure how they should be used and interpreted. In
this article we illustrate some basic features of error bars and explain
how they can help communicate data and assist correct interpretation.
Error bars may show confidence intervals, standard errors, standard
deviations, or other quantities. Different types of error bars give
quite different information, and so figure legends must make clear what
error bars represent. We suggest eight simple rules to assist with
effective use and interpretation of error bars.
5/1/2014: Miniaturize your NMR machine - resonance on a chip
Zalesskiy SS, Danieli E, Blümich B, Ananikov VP
Miniaturization of NMR Systems: Desktop Spectrometers, Microcoil Spectroscopy, and “NMR on a Chip” for Chemistry, Biochemistry, and Industry
Chemical Reviews 114: 5641-5694 (2014)