Bacterial symbionts have long been suspected to be the true producers of many drug candidates isolated from marine invertebrates. Sponges, the most important marine source of biologically active natural products, have been frequently hypothesized to contain compounds of bacterial origin. This symbiont hypothesis, however, remained unproven because of a general inability to cultivate the suspected producers. However, we have recently identified an uncultured Pseudomonas sp. symbiont as the most likely producer of the defensive antitumor polyketide pederin in Paederus fuscipes beetles by cloning the putative biosynthesis genes. Here we report closely related genes isolated from the highly complex metagenome of the marine sponge Theonella swinhoei, which is the source of the onnamides and theopederins, a group of polyketides that structurally resemble pederin. Sequence features of the isolated genes clearly indicate that it belongs to a prokaryotic genome and should be responsible for the biosynthesis of almost the entire portion of the polyketide structure that is correlated with antitumor activity. Besides providing further proof for the role of the related beetle symbiont-derived genes, these findings raise intriguing ecological and evolutionary questions and have important general implications for the sustainable production of otherwise inaccessible marine drugs by using biotechnological strategies. F or almost 30 years, symbiotic bacteria have been discussed as the likely true producers of numerous natural products isolated from marine invertebrates (1). Particularly suggestive of a bacterial origin is the similarity of many compounds from sponges, tunicates, or bryozoans to complex polyketides and nonribosomal peptides, two groups of metabolites that are otherwise known exclusively from microorganisms (2, 3). Into these structural families fall some of today's most promising drug candidates, such as discodermolide, bryostatin 1, aplidine, and ET-743 (4). The existence of producing symbionts could have far reaching consequences for the development of sustainable, fermentation-based sources of invertebrate-derived drug candidates, almost all of which are currently inaccessible in large amounts. Several studies have tried to pinpoint the producers by using cultivation (5), cell separation (6), immunolocalization (7), or in situ hybridization (8) approaches. However, as none of these methods have so far provided unambiguous results, the true origin of the compounds still remains an enigma. We have recently used a genetic strategy to provide insights into natural product symbiosis in terrestrial insects (9). Rove beetles of the genera Paederus and Paederidus are the source of the highly active antitumor polyketide pederin (Fig. 1), which they use as chemical defense (10). We isolated a set of putative pederin biosynthesis genes (9, 11) from the metagenome of Paederus fuscipes beetles and traced them to a bacterial symbiont with the closest relationship to Pseudomonas aeruginosa (12). The genes encode a mixed modul...

Symbiotic bacteria have long been proposed as being responsible for the production of numerous natural products isolated from invertebrate animals. However, systematic studies of invertebrate-symbiont associations are usually associated with serious technical challenges, such as the general resistance of symbionts to culturing attempts and the complexity of many microbial consortia. Herein an overview is provided on the culture-independent, metagenomic strategies recently employed by our group to contribute to a better understanding of natural product symbiosis. Using terrestrial Paederus spp. beetles and the marine sponge Theonella swinhoei as model animals, the putative genes responsible for the production of pederin-type antitumor polyketides have been isolated. In Paederus fuscipes, which uses pederin for chemical defense, these genes belong to an as-yet unculturable symbiont closely related to Pseudomonas aeruginosa. To study the extremely complex association of T. swinhoei and its multispecies bacterial consortium, we used a phylogenetic approach that allowed the isolation of onnamide/theopederin polyketide synthase genes from an uncultured sponge symbiont. Analysis of the biosynthesis genes provided unexpected insights into a possible evolution of pederin-type pathways. Besides revealing new facets of invertebrate chemical ecology, these first gene clusters from uncultivated symbiotic producers suggest possible biotechnological strategies to solve the supply problem associated with the development of most marine drug candidates.

Numerous marine sponges harbor enormous amounts of as-yet-uncultivated bacteria in their tissues. There is increasing evidence that these symbionts play an important role in the synthesis of protective metabolites, many of which are of great pharmacological interest. In this study, genes for the biosynthesis of polyketides, one of the most important classes of bioactive natural products, were systematically investigated in 20 demosponge species from different oceans. Unexpectedly, the sponge metagenomes were dominated by a ubiquitously present, evolutionarily distinct, and highly sponge-specific group of polyketide synthases (PKSs). Open reading frames resembling animal fatty acid genes were found on three corresponding DNA regions isolated from the metagenomes of Theonella swinhoei and Aplysina aerophoba. Their architecture suggests that methyl-branched fatty acids are the metabolic product. According to a phylogenetic analysis of housekeeping genes, at least one of the PKSs belongs to a bacterium of the Deinococcus-Thermus phylum. The results provide new insights into the chemistry of sponge symbionts and allow inference of a detailed phylogeny of the diverse functional PKS types present in sponge metagenomes. Based on these qualitative and quantitative data, we propose a significantly simplified strategy for the targeted isolation of biomedically relevant PKS genes from complex sponge-symbiont associations.

On the occasion of the 20th anniversary of the Center for Alternative Methods to Animal Experiments (ZEBET), an international symposium was held at the German Federal Institute for Risk Assessment (BfR) in Berlin. At the same time, this symposium was meant to celebrate the 50th anniversary of the publication of the book “The Principles of Humane Experimental Technique” by Russell and Burch in 1959 in which the 3Rs principle (that is, Replacement, Reduction, and Refinement) has been coined and introduced to foster the development of alternative methods to animal testing. Another topic addressed by the symposium was the new vision on “Toxicology in the twenty-first Century”, as proposed by the US-National Research Council, which aims at using human cells and tissues for toxicity testing in vitro rather than live animals. An overview of the achievements and current tasks, as well as a vision of the future to be addressed by ZEBET@BfR in the years to come is outlined in the present paper.

No abstract

In this paper, we are going to present a method for detecting the risks of patent infringement by evaluating similarities between patent documents on the basis of semantic patent analysis. This approach enables the user to visualize similarities in the contents on a semantic patent map by means of multi‐dimensional scaling. The effectiveness of the semantic patent map has already been demonstrated by Dressler (2006) with regard to patents of seal technology, in which documents are commonly kept short and the extracted contents are concise. This paper will open out to the field of biotechnology, where patents can easily comprise several hundreds of pages. The method presented here conveys an interdisciplinary approach and combines computer‐aided natural language processing with domain‐specific expertise of biochemical processes. This is illustrated by an authentic case of infringement involving two manufacturers of DNA chips. Our experiment will show how the infringement case is visualized on a patent map based on semantic patent analysis. This experiment can be compared with the search for a needle in a haystack, the two competitive patents representing significantly conflicting ‘needles.’ From an approximate number of 4,000 patents in the current US Class 435/6, a set of patents was selected that included the ‘needles’ mentioned. This paper will point out how such mutual interference can be detected by way of semantic patent analysis, and what advice may be given to R&D managers who are faced with the risk of patent infringement.

Marine snails of the genus Aplysia possess numerous bioactive substances. We have purified a 60 kDa protein, APIT (Aplysia punctata ink toxin), from the defensive ink of A. punctata that triggers cell death with profound tumor specificity. Tumor cell death induced by APIT is independent of apoptosis but is characterized by the rapid loss of metabolic activity, membrane permeabilization, and shrinkage of nuclei. Proteome analysis of APIT-treated tumor cells indicated a modification of peroxiredoxin I, a cytoplasmic peroxidase involved in the detoxification of peroxides. Interestingly, knockdown of peroxiredoxin I expression by RNA interference sensitized cells for APIT-induced cell death. APIT induced the death of tumor cells via the enzymatic production of H 2 O 2 and catalase completely blocked APITs' activity. Our data suggest that H 2 O 2 induced stress and the modulation of peroxiredoxins might be a promising approach for tumor therapy.

Rhetorical elements from scientific publications provide a more structured view of the document and allow algorithms to focus on particular parts of the text. We surveyed the literature for previously proposed schemes for rhetorical elements and present an overview of its current state of the art. We also searched for available tools using these schemes and applied four tools for our particular task of ranking biomedical abstracts based on text similarity. Comparison of the tools with two strong baselines shows that the predictions provided by the ArguminSci tool can support our use case of mining alternative methods for animal experiments.