Automatic identification of novel bacteria using Raman spectroscopy and Gaussian processes.

Raman spectroscopy is successfully used for the reliable classification of complex biological samples. Much effort concentrates on the accurate prediction of known categories for highly relevant tasks in a wide area of applications such as cancer detection and bacteria recognition. However, the resulting recognition systems cannot always be directly used in practice since unseen samples might not belong to classes present in the training set. Our work aims to tackle this problem of novelty detection using a recently proposed approach based on Gaussian processes. By learning novelty scores for a large bacteria Raman dataset comprising 50 different strains, we analyze the behavior of this method on an independent dataset which includes known as well as unknown categories. Our experiment reveals that non-parametric methods such as Gaussian processes can be successfully applied to the task of finding unknown bacterial strains, leading to encouraging results motivating their further utilization in this area.

Production of a new thiopeptide antibiotic, TP-1161, by a marine Nocardiopsis species.

Twenty-seven marine sediment- and sponge-derived actinomycetes with a preference for or dependence on seawater for growth were classified at the genus level using molecular taxonomy. Their potential to produce bioactive secondary metabolites was analyzed by PCR screening for genes involved in polyketide and nonribosomal peptide antibiotic synthesis. Using microwell cultures, conditions for the production of antibacterial and antifungal compounds were identified for 15 of the 27 isolates subjected to this screening. Nine of the 15 active extracts were also active against multiresistant gram-positive bacterial and/or fungal indicator organisms, including vancomycin-resistant Enterococcus faecium and multidrug-resistant Candida albicans. Activity-guided fractionation of fermentation extracts of isolate TFS65-07, showing strong antibacterial activity and classified as a Nocardiopsis species, allowed the identification and purification of the active compound. Structure elucidation revealed this compound to be a new thiopeptide antibiotic with a rare aminoacetone moiety. The in vitro antibacterial activity of this thiopeptide, designated TP-1161, against a panel of bacterial strains was determined.

Complete control of regioselectivity in the intramolecular [2 + 2] photocycloaddition of 2-alkenyl-3(2H)-furanones by the length of the side chain.

The 2-(omega-alkenyl)-substituted 2-methyl-3(2H)-furanones 2a and 2b were prepared from biacetyl (3) in four reaction steps and in overall yields of 20% and 21%, respectively. They underwent a clean intramolecular [2 + 2] photocycloaddition upon irradiation at lambda = 350 nm. Whereas compound 2a reacted in the expected manner and yielded 7-oxabicyclo[3.2.1.0(3,6)]octane 7 (87% yield), the regioselectivity in the photocycloaddition of compound 2b was completely reversed. The reaction led to compound 8 (92% yield) with the unusual 9-oxabicyclo[4.2.1.0(3,8)]nonane skeleton, the structure of which was established by single-crystal X-ray crystallography.