Tools, Methods & Assays

As Europe’s flagship laboratory for molecular biology, EMBL-inventions are scattered across the whole range of molecular biology research.

The technologies cover areas including protein expression tools, nanotechnology, research tools & platforms, kit-ready assays, diagnostic tools and targets that can be further developed into future drugs.

LiMA, a liposome microarray to systematically study protein lipid interactions

The interaction of proteins with lipids is of fundamental importance in most cellular process. To date it is studied by either testing protein-lipid binding affinity towards a very limited number of ~10-20 individual lipids (mostly phospholipids) spotted on a membrane. This is not physiological, as the lipids do not form membrane bilayers, and does not take into account cooperative mechanisms, as lipids can be probed only one-by-one and not in complex combination. Methods based on the use of artificial surrogate membranes only partially resolve these issues, and their fabrication, storage and handling are difficult, they are not readily scalable, often require non-physiological buffers with lipid-specific adjustments, use large amounts of lipids and purified proteins, which precludes their use in large and systematic analyses. Considering that a eukaryotic cell produces more than 1000 different lipid species, each with distinct properties and often acting in combination, a tool is needed that enables the study of protein-lipid interaction in a manner that is on a par with the functional genomics resources now available, i.e. a simple device to comprehensively study protein-lipid interaction in a physiological, sensitive, reproducible, cooperative and high-throughput manner. LiMA is a mircoarray chip to measure protein recruitment to membranes that satisfies this need.

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microRNA miR-142 as pluripotent stem cell marker

Pluripotent stem cells (PSCs) play an important role especially in the areas of regenerative medicine and drug discovery. One of the challenges in working with pluripotent stem cells is to control the states of pluripotency and differentiation uniformly within one culture. The microRNA miR-142 was shown to be a switch for the differentiation state of PSCs.

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ESPRIT, a systematic approach for generating soluble protein variants

Proteins often express insolubly which severely limits their usefulness in areas such as structural analysis by crystallography and NMR. Several systems have been described that aim to identify soluble protein variants generated by random mutagenesis or truncation. These methods usually involve fusion of a C-terminal “solubility reporter” (e.g. GFP, CAT or beta galactosidase). The tag used in the methods described above are large and thus enhance the solubility profile of the fusion product. The solubility of the thus created fusion protein is highly dependent on the solubility phenotype of the tag used. By using a smaller tag the solubility influence of the tag is reduced leading to a reduction of false positives.

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Cell-based method for the analysis of protein-protein interactions

Protein-protein interactions are crucial for virtually all cellular processes. Therefore analysis of such interactions is becoming increasingly important in molecular biology, biochemistry and computational biology. Furthermore, disturbed protein-protein interactions can contribute to diseases rendering the identification of protein-protein interaction inhibitors highly desirable in drug discovery. Traditional technologies used for analysis of protein-protein interactions share the major drawback that the experimental set-up is highly artificial, questioning the physiological relevance of such interactions in vivo. The technology presented here allows for reliable analysis of intracellular protein-protein interactions based on a translocation principle.

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Novel biomarkers for the detection of testicular carcinoma in situ and derived cancers in human samples

Virtually all testicular cancers originate from the same precursor, the carcinoma in situ (CIS) cell. If left untreated, CIS will invariably progress into testicular cancer. Unfortunately, the disease is rarely diagnosed at this asymptomatic stage, since it hitherto has required a testicular biopsy to identify CIS. The aim of the current work is to develop and validate a non-invasive diagnostic test for early detection of testicular cancer based on identification of pre-invasive CIS cells in semen samples.

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Phasing macromolecular structures by UV-induced damage

This invention relates to a novel method to phase macromolecular crystal structures using damage induced by UV radiation (UV-RIP). Compared to existing techniques this method shows the advantage that it can be performed on a single crystal of the native protein and introduces only specific changes. The technology can be used independently of a synchrotron.

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