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Patent
CSIC - Institute of Refrigeration and Embl European Molecular Biology Laboratory | Date: 2017-02-08

The invention provides an isolated multiple integration element (MIE) comprising, in the specified order: a) a homing endonuclease site (HE); b) a promoter selected from the group consisting of AOX1, FLD1, FMD1, GAP and TEF1; c) a BstBI restriction site; d) a sequence encoding a secretion signal; e) a Ncol restriction site; f) a selection marker gene; g) a Pmel restriction site; h) a DNA sequence encoding a detection and/or purification polypeptide; i) a terminator selected from the group consisting of AOX1, FLD1, FMD1, GAP and TEF1; and j) a BstXI restriction site, wherein the HE and BstXI sites are selected such that HE and BstXI result in compatible cohesive ends when cut by the homing endonuclease and the BstXI restriction enzyme, respectively, and the ligation product of HE and BstXI cohesive ends can neither be cleaved by the homing endonuclease nor the BstXI restriction enzyme.


Patent
Leica and Embl European Molecular Biology Laboratory | Date: 2017-02-07

A method for scanning a sample using an electrically or electronically controllable microscope includes performing a continuous scanning of the sample so as to repeatedly generate a plurality of images of the sample, each of the plurality of images corresponding to a different time, the microscope being controlled via a control computer during the scanning. The plurality of images are analyzed using at least one second computer connected via a network, wherein the at least one second computer is configured to classify each of the plurality of images as one of interesting and non-interesting while the continuous scanning of the sample with the microscope continues. The continuous scanning of the sample is automatically influenced based on the classifying of the images performed by the at least one second computer.


Afonin S.,Karlsruhe Institute of Technology | Glaser R.W.,Friedrich - Schiller University of Jena | Sachse C.,EMBL European Molecular Biology Laboratory | Salgado J.,University of Valencia | And 2 more authors.
Biochimica et Biophysica Acta - Biomembranes | Year: 2014

Many amphiphilic antimicrobial peptides permeabilize bacterial membranes via successive steps of binding, re-alignment and/or oligomerization. Here, we have systematically compared the lipid interactions of two structurally unrelated peptides: the cyclic β-pleated gramicidin S (GS), and the α-helical PGLa. 19F NMR was used to screen their molecular alignment in various model membranes over a wide range of temperatures. Both peptides were found to respond to the phase state and composition of these different samples in a similar way. In phosphatidylcholines, both peptides first bind to the bilayer surface. Above a certain threshold concentration they can re-align and immerse more deeply into the hydrophobic core, which presumably involves oligomerization. Re-alignment is most favorable around the lipid chain melting temperature, and also promoted by decreasing bilayer thickness. The presence of anionic lipids has no influence in fluid membranes, but in the gel phase the alignment states are more complex. Unsaturated acyl chains and other lipids with intrinsic negative curvature prevent re-alignment, hence GS and PGLa do not insert into mixtures resembling bacterial membranes, nor into bacterial lipid extracts. Cholesterol, which is present in high concentrations in animal membranes, even leads to an expulsion of the peptides from the bilayer and prevents their binding altogether. However, a very low cholesterol content of 10% was found to promote binding and re-alignment of both peptides. Overall, these findings show that the ability of amphiphilic peptides to re-align and immerse into a membrane is determined by the physico-chemical properties of the lipids, such as spontaneous curvature. This idea is reinforced by the remarkably similar behavior observed here for two structurally unrelated molecules (with different conformation, size, shape, charge), which further suggests that their activity at the membrane level is largely governed by the properties of the constituent lipids, while the selectivity towards different cell types is additionally ruled by electrostatic attraction between peptide and cell surface. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova. © 2014 Elsevier B.V.


Afonin S.,Karlsruhe Institute of Technology | Glaser R.W.,Friedrich - Schiller University of Jena | Sachse C.,EMBL European Molecular Biology Laboratory | Salgado J.,University of Valencia | And 2 more authors.
Biochimica et biophysica acta | Year: 2014

Many amphiphilic antimicrobial peptides permeabilize bacterial membranes via successive steps of binding, re-alignment and/or oligomerization. Here, we have systematically compared the lipid interactions of two structurally unrelated peptides: the cyclic β-pleated gramicidin S (GS), and the α-helical PGLa. (19)F NMR was used to screen their molecular alignment in various model membranes over a wide range of temperatures. Both peptides were found to respond to the phase state and composition of these different samples in a similar way. In phosphatidylcholines, both peptides first bind to the bilayer surface. Above a certain threshold concentration they can re-align and immerse more deeply into the hydrophobic core, which presumably involves oligomerization. Re-alignment is most favorable around the lipid chain melting temperature, and also promoted by decreasing bilayer thickness. The presence of anionic lipids has no influence in fluid membranes, but in the gel phase the alignment states are more complex. Unsaturated acyl chains and other lipids with intrinsic negative curvature prevent re-alignment, hence GS and PGLa do not insert into mixtures resembling bacterial membranes, nor into bacterial lipid extracts. Cholesterol, which is present in high concentrations in animal membranes, even leads to an expulsion of the peptides from the bilayer and prevents their binding altogether. However, a very low cholesterol content of 10% was found to promote binding and re-alignment of both peptides. Overall, these findings show that the ability of amphiphilic peptides to re-align and immerse into a membrane is determined by the physico-chemical properties of the lipids, such as spontaneous curvature. This idea is reinforced by the remarkably similar behavior observed here for two structurally unrelated molecules (with different conformation, size, shape, charge), which further suggests that their activity at the membrane level is largely governed by the properties of the constituent lipids, while the selectivity towards different cell types is additionally ruled by electrostatic attraction between peptide and cell surface. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova. Copyright © 2014 Elsevier B.V. All rights reserved.


PubMed | EMBL European Molecular Biology Laboratory, HITS Heidelberg Institute for Theoretical Studies and SEMBL European Molecular Biology Laboratory
Type: Comparative Study | Journal: The journal of physical chemistry. B | Year: 2015

Understanding the function of intrinsically disordered proteins is intimately related to our capacity to correctly sample their conformational dynamics. So far, a gap between experimentally and computationally derived ensembles exists, as simulations show overcompacted conformers. Increasing evidence suggests that the solvent plays a crucial role in shaping the ensembles of intrinsically disordered proteins and has led to several attempts to modify water parameters and thereby favor protein-water over protein-protein interactions. This study tackles the problem from a different perspective, which is the use of the Kirkwood-Buff theory of solutions to reproduce the correct conformational ensemble of intrinsically disordered proteins (IDPs). A protein force field recently developed on such a basis was found to be highly effective in reproducing ensembles for a fragment from the FG-rich nucleoporin 153, with dimensions matching experimental values obtained from small-angle X-ray scattering and single molecule FRET experiments. Kirkwood-Buff theory presents a complementary and fundamentally different approach to the recently developed four-site TIP4P-D water model, both of which can rescue the overcollapse observed in IDPs with canonical protein force fields. As such, our study provides a new route for tackling the deficiencies of current protein force fields in describing protein solvation.


Granovskaia M.V.,EMBL European Molecular Biology Laboratory | Jensen L.J.,EMBL European Molecular Biology Laboratory | Jensen L.J.,Novo Nordisk AS | Ritchie M.E.,University of Cambridge | And 7 more authors.
Genome Biology | Year: 2010

Background: Extensive transcription of non-coding RNAs has been detected in eukaryotic genomes and is thought to constitute an additional layer in the regulation of gene expression. Despite this role, their transcription through the cell cycle has not been studied; genome-wide approaches have only focused on protein-coding genes. To explore the complex transcriptome architecture underlying the budding yeast cell cycle, we used 8 bp tiling arrays to generate a 5 minute-resolution, strand-specific expression atlas of the whole genome.Results: We discovered 523 antisense transcripts, of which 80 cycle or are located opposite periodically expressed mRNAs, 135 unannotated intergenic non-coding RNAs, of which 11 cycle, and 109 cell-cycle-regulated protein-coding genes that had not previously been shown to cycle. We detected periodic expression coupling of sense and antisense transcript pairs, including antisense transcripts opposite of key cell-cycle regulators, like FAR1 and TAF2.Conclusions: Our dataset presents the most comprehensive resource to date on gene expression during the budding yeast cell cycle. It reveals periodic expression of both protein-coding and non-coding RNA and profiles the expression of non-annotated RNAs throughout the cell cycle for the first time. This data enables hypothesis-driven mechanistic studies concerning the functions of non-coding RNAs. © 2010 Granovskaia et al.; licensee BioMed Central Ltd.


Patent
Embl European Molecular Biology Laboratory and Thoraxklinik Heidelberg GmbH | Date: 2011-01-05

The present invention relates to a method for diagnosing the risk of cancer recurrence in a mammalian patient, comprising detecting the expression of macroH2A1.1 and/or macroH2A2 in a biological sample obtained from said patient, wherein a low or reduced expression of said macroH2A1.1 and/or macroH2A2 is indicative for an increased risk of cancer recurrence in said patient. The present invention is further directed at improved methods for treating cancer, in particular breast and/or lung cancer, based on said diagnostic method.


Spornraft M.,TU Munich | Kirchner B.,TU Munich | Haase B.,EMBL European Molecular Biology Laboratory | Benes V.,EMBL European Molecular Biology Laboratory | And 2 more authors.
PLoS ONE | Year: 2014

There are several protocols and kits for the extraction of circulating RNAs from plasma with a following quantification of specific genes via RT-qPCR. Due to the marginal amount of cell-free RNA in plasma samples, the total RNA yield is insufficient to perform Next-Generation Sequencing (NGS), the state-of-the-art technology in massive parallel sequencing that enables a comprehensive characterization of the whole transcriptome. Screening the transcriptome for biomarker signatures accelerates progress in biomarker profiling for molecular diagnostics, early disease detection or food safety. Therefore, the aim was to optimize a method that enables the extraction of sufficient amounts of total RNA from bovine plasma to generate good-quality small RNA Sequencing (small RNA-Seq) data. An increased volume of plasma (9 ml) was processed using the Qiagen miRNeasy Serum/Plasma Kit in combination with the QIAvac24 Plus system, a vacuum manifold that enables handling of high volumes during RNA isolation. 35 ng of total RNA were passed on to cDNA library preparation followed by small RNA high-throughput sequencing analysis on the Illumina HiSeq2000 platform. Raw sequencing reads were processed by a data analysis pipeline using different free software solutions. Seq-data was trimmed, quality checked, gradually selected for miRNAs/piRNAs and aligned to small RNA reference annotation indexes. Mapping to human reference indexes resulted in 4.8±2.8% of mature miRNAs and 1.4±0.8% of piRNAs and of 5.0±2.9% of mature miRNAs for bos taurus. © 2014 PLOS ONE.


Patent
Embl European Molecular Biology Laboratory | Date: 2013-08-16

The present invention relates to an activator of the calcineurin subunit A1 isofomi (C_(n)A1) or of the C-terminal domain of the calcineurin subunit A1 isofomi (C_(n)A1) for the production of a medicament for the modulation of myocardial growth without adversely affecting contractile function.


PubMed | EMBL European Molecular Biology Laboratory and TU Munich
Type: Journal Article | Journal: PloS one | Year: 2014

There are several protocols and kits for the extraction of circulating RNAs from plasma with a following quantification of specific genes via RT-qPCR. Due to the marginal amount of cell-free RNA in plasma samples, the total RNA yield is insufficient to perform Next-Generation Sequencing (NGS), the state-of-the-art technology in massive parallel sequencing that enables a comprehensive characterization of the whole transcriptome. Screening the transcriptome for biomarker signatures accelerates progress in biomarker profiling for molecular diagnostics, early disease detection or food safety. Therefore, the aim was to optimize a method that enables the extraction of sufficient amounts of total RNA from bovine plasma to generate good-quality small RNA Sequencing (small RNA-Seq) data. An increased volume of plasma (9 ml) was processed using the Qiagen miRNeasy Serum/Plasma Kit in combination with the QIAvac24 Plus system, a vacuum manifold that enables handling of high volumes during RNA isolation. 35 ng of total RNA were passed on to cDNA library preparation followed by small RNA high-throughput sequencing analysis on the Illumina HiSeq2000 platform. Raw sequencing reads were processed by a data analysis pipeline using different free software solutions. Seq-data was trimmed, quality checked, gradually selected for miRNAs/piRNAs and aligned to small RNA reference annotation indexes. Mapping to human reference indexes resulted in 4.82.8% of mature miRNAs and 1.40.8% of piRNAs and of 5.02.9% of mature miRNAs for bos taurus.

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