Recent Publications

Description

Lysosome-associated membrane glycoprotein 3 (LAMP3) is a type I transmembrane protein of the LAMP protein family with a cell-type-specific expression in alveolar type II cells in mice and hitherto unknown function. In type II pneumocytes, LAMP3 is localized in lamellar bodies, secretory organelles releasing pulmonary surfactant into the extracellular space to lower surface tension at the air/liquid interface. The physiological function of LAMP3, however, remains enigmatic. We generated Lamp3 knockout mice by CRISPR/Cas9. LAMP3 deficient mice are viable with an average life span and display regular lung function under basal conditions. The levels of a major hydrophobic protein component of pulmonary surfactant, SP-C, are strongly increased in the lung of Lamp3 knockout mice, and the lipid composition of the bronchoalveolar lavage shows mild but significant changes, resulting in alterations in surfactant functionality. In ovalbumin-induced experimental allergic asthma, the changes in lipid composition are aggravated, and LAMP3-deficient mice exert an increased airway resistance. Our data suggest a critical role of LAMP3 in the regulation of pulmonary surfactant homeostasis and normal lung function.

This shotgun lipidomics data set includes the raw unimputed lipidomics values for lung tissue and bronchoalveolar fluid in mol percentage as well as on a per protein content base. Data can be found in the LAMP3_LipidomicsRawData.xlsx file.
Description and details of sample extraction to data processing procedures are included in the LAMP3_Processing.xlsx file. Additional project files for LipidXplorer and the complementary MFQL files are included in the corresponding folders.

Data Archive:

LAMP3OnlineRepository.zip

Publications:

Lars P. Lunding, Daniel Krause, Guido Stichtenoth, Cordula Stamme, Niklas Lauterbach, Jan Hegermann, Matthias Ochs, Björn Schuster, Radislav Sedlacek, Paul Saftig, Dominik Schwudke, Michael Wegmann, Markus Damme. LAMP3 is critical for surfactant homeostasis in mice, doi:10.1101/2021.02.05.429758

Preliminary LipidCompass accession number: LCE7

Abstract

We introduce Goslin, a polyglot grammar for common lipid shorthand nomenclatures based on the LIPID MAPS nomenclature and the shorthand nomenclature established by Liebisch and co-authors and used by LipidHome and SwissLipids. Goslin was designed to address the following pressing issues in the lipidomics field: 1) to simplify the implementation of lipid name handling for developers of mass spectrometry-based lipidomics tools; 2) to offer a tool that unifies and normalizes the main existing lipid name dialects enabling a lipidomics analysis in a high-throughput fashion and 3) to provide a consistent mapping from lipid shorthand names to lipid building blocks and structural properties. We provide implementations of Goslin in four major programming languages, namely C++, Java, Python 3, and R to kick-start adoption and integration. Further, we set up a web service for users to work with Goslin directly. All implementations are available free of charge under a permissive open source license.

 

Kopczynski, D., Hoffmann, N., et al. Goslin - A Grammar of Succinct Lipid Nomenclature. Analytical Chemistry, 92, 16, 10957–10960 , June 26th, (2020)
doi:10.1021/acs.analchem.0c01690

LipidCreator workbench to probe the lipidomic landscape

Abstract

Mass spectrometry (MS)-based targeted lipidomics enables the robust quantification of selected lipids under various biological conditions but comprehensive software tools to support such analyses are lacking. Here we present LipidCreator, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LipidCreator provides all functionalities needed to define fragments, manage stable isotope labeling, optimize collision energy and generate in silico spectral libraries. We validate LipidCreator assays computationally and analytically and prove that it is capable to generate large targeted experiments to analyze blood and to dissect lipid-signaling pathways such as in human platelets.

 

Peng, B. et al. LipidCreator workbench to probe the lipidomic landscape. Nature Communications 11, 2057 (2020)
doi:10.1038/s41467-020-15960-z

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

Abstract

The German Network for Bioinformatics Infrastructure (de.NBI) is a national and academic infrastructure funded by the German Federal Ministry of Education and Research (BMBF). The de.NBI provides (i) service, (ii) training, and (iii) cloud computing to users in life sciences research and biomedicine in Germany and Europe and (iv) fosters the cooperation of the German bioinformatics community with international network structures. The de.NBI members also run the German node (ELIXIR-DE) within the European ELIXIR network. The de.NBI / ELIXIR-DE training platform, also known as special interest group 3 (SIG 3) ‘Training & Education’, coordinates the bioinformatics training of de.NBI and the German ELIXIR node. The network provides a high-quality, coherent, timely, and impactful training program across its eight service centers. Life scientists learn how to handle and analyze biological big data more effectively by applying tools, standards and compute services provided by de.NBI. Since 2015, more than 250 training courses were carried out with more than 5,200 participants and these courses received recommendation rates of almost 90% (status as of October 2019). In addition to face-to-face training courses, online training was introduced on the de.NBI website in 2016 and guidelines for the preparation of e-learning material were established in 2018. In 2016, ELIXIR-DE joined the ELIXIR training platform. Here, the de.NBI / ELIXIR-DE training platform collaborates with ELIXIR in training activities, advertising training courses via TeSS and discussions on the exchange of data for training events essential for quality assessment on both the technical and administrative levels. The de.NBI training program trained thousands of scientists from Germany and beyond in many different areas of bioinformatics.

 

Wibberg, D. et al. The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR. ELIXIR F1000(2019)
doi:10.12688/f1000research.20244.1