scholarly journals LION/web: a web-based ontology enrichment tool for lipidomic data analysis

GigaScience ◽  
2019 ◽  
Vol 8 (6) ◽  
Author(s):  
Martijn R Molenaar ◽  
Aike Jeucken ◽  
Tsjerk A Wassenaar ◽  
Chris H A van de Lest ◽  
Jos F Brouwers ◽  
...  
Keyword(s):  
Membrane Fluidity ◽  
Plasma Membranes ◽  
Chinese Hamster Ovary Cells ◽  
Chinese Hamster ◽  
Lateral Diffusion ◽  
Decanoic Acid ◽  
Web Based ◽  
Ovary Cells ◽  
Lipid Species ◽  
Significant Enrichment

Abstract Background A major challenge for lipidomic analyses is the handling of the large amounts of data and the translation of results to interpret the involvement of lipids in biological systems. Results We built a new lipid ontology (LION) that associates >50,000 lipid species to biophysical, chemical, and cell biological features. By making use of enrichment algorithms, we used LION to develop a web-based interface (LION/web, www.lipidontology.com) that allows identification of lipid-associated terms in lipidomes. LION/web was validated by analyzing a lipidomic dataset derived from well-characterized sub-cellular fractions of RAW 264.7 macrophages. Comparison of isolated plasma membranes with the microsomal fraction showed a significant enrichment of relevant LION-terms including “plasma membrane", “headgroup with negative charge", "glycerophosphoserines", “above average bilayer thickness", and “below average lateral diffusion". A second validation was performed by analyzing the membrane fluidity of Chinese hamster ovary cells incubated with arachidonic acid. An increase in membrane fluidity was observed both experimentally by using pyrene decanoic acid and by using LION/web, showing significant enrichment of terms associated with high membrane fluidity ("above average", "very high", and "high lateral diffusion" and "below average transition temperature"). Conclusions The results demonstrate the functionality of LION/web, which is freely accessible in a platform-independent way.

scholarly journals LION/web: a web-based ontology enrichment tool for lipidomic data analysis

2018 ◽  
Author(s):  
Martijn R. Molenaar ◽  
Aike Jeucken ◽  
Tsjerk A. Wassenaar ◽  
Chris H. A. van de Lest ◽  
Jos F. Brouwers ◽  
...  
Keyword(s):  
Membrane Fluidity ◽  
Plasma Membranes ◽  
Lateral Diffusion ◽  
Decanoic Acid ◽  
Web Based ◽  
Raw 264.7 Macrophages ◽  
Lipid Species ◽  
Significant Enrichment ◽  
Average Transition ◽  
Very High

SUMMARYA major challenge for lipidomic analyses is the handling of the large amounts of data and the translation of results to interpret the involvement of lipids in biological systems. We built a new lipid ontology (LION) that associates over 50,000 lipid species to biophysical, chemical and cell biological features. By making use of enrichment algorithms, we used LION to develop a web-based interface (LION/web, www.lipidontology.com) that allows identification of lipid-associated terms in lipidomes. LION/web was validated by analyzing a lipidomic dataset derived from well-characterized sub-cellular fractions of RAW 264.7 macrophages. Comparison of isolated plasma membranes with the microsomal fraction showed a significant enrichment of relevant LION-terms including ‘plasma membrane’, ‘headgroup with negative charge, ‘glycerophosphoserines’, ‘above average bilayer thickness’, and ‘below average lateral diffusion’. A second validation was performed by analyzing the membrane fluidity of CHO cells incubated with arachidonic acid. An increase in membrane fluidity was observed both experimentally by using pyrene decanoic acid and by using LION/web, showing significant enrichment of terms associated with high membrane fluidity ('above average’, 'very high’ and 'high lateral diffusion’, and 'below average transition temperature’). The results demonstrate the functionality of LION/web, which is freely accessible in a platform-independent way.

scholarly journals Phosphorylation of high-molecular-weight membrane protein species in Chinese-hamster ovary cells in culture: effect of 6-N,2′-O-dibutyryladenosine 3′:5′-cyclic monophosphate plus testosterone (Short Communication)

1973 ◽  
Vol 132 (3) ◽  
pp. 641-644 ◽  
Author(s):  
Manuel Rieber ◽  
Josefina Bacalao
Keyword(s):  
Chinese Hamster Ovary ◽  
Plasma Membranes ◽  
Short Communication ◽  
Chinese Hamster Ovary Cells ◽  
Chinese Hamster ◽  
Protein Species ◽  
Ovary Cells ◽  
Molecular Weights ◽  
Qualitative Pattern ◽  
Phosphate Incorporation

Growth of Chinese-hamster ovary cells in [32P]phosphate and [3H]leucine and subsequent assay of the plasma membranes reveals phosphorylation in two protein regions corresponding to molecular weights of 280000 and 195000. Culture in the presence of the 6-N,2-O′-dibutyryl derivative of cyclic AMP plus testosterone does not stimulate [32P]-phosphate incorporation, but determines a modification in the qualitative pattern of phosphorylation.

The Isolation and Characterization of the Plasma Membrane of Cultured Chinese Hamster Ovary Cells

1975 ◽  
Vol 53 (8) ◽  
pp. 914-920 ◽  
Author(s):  
R. L. Juliano ◽  
E. Gagalang
Keyword(s):  
Plasma Membrane ◽  
Chinese Hamster Ovary ◽  
Plasma Membranes ◽  
Chinese Hamster Ovary Cells ◽  
Polymer System ◽  
Chinese Hamster ◽  
Two Phase ◽  
Ovary Cells ◽  
Isolation And Characterization ◽  
Chemical Assay

Plasma membranes were prepared from cultured Chinese hamster ovary cells utilizing a two-phase polymer system and were characterized by enzymatic and chemical assay, and by electron microscopy. The usual degree of purification of presumptive membrane markers such as Na+–K+ ATPase (ATP phosphohydrolase, EC 3.6.1.3) ranged from three-to eightfold. Gel electrophoresis in SDS revealed several polypeptides and two glycopeptides which were enriched in the plasma membrane fraction.

Recombinant Human Soluble Thrombomodulin Delivers Bounded Thrombin to Antithrombin III: Thrombomodulin Associates with Free Thrombin and Is Recycled to Activate Protein C

1993 ◽  
Vol 70 (03) ◽  
pp. 418-422 ◽  
Author(s):  
Masaharu Aritomi ◽  
Naoko Watanabe ◽  
Rika Ohishi ◽  
Komakazu Gomi ◽  
Takao Kiyota ◽  
...  
Keyword(s):  
Protein C ◽  
Antithrombin Iii ◽  
Transmembrane Domain ◽  
Chinese Hamster Ovary Cells ◽  
Time Lag ◽  
Chinese Hamster ◽  
Ovary Cells ◽  
Soluble Thrombomodulin ◽  
Simulation Based ◽  
Recombinant Human Soluble Thrombomodulin

SummaryRecombinant human soluble thrombomodulin (rhs-TM), having no transmembrane domain or chondroitin sulfate, was expressed in Chinese hamster ovary cells. Interactions between rhs-TM, thrombin (Th), protein C (PC) and antithrombin III (ATIII) were studied. Equilibrium between rhs-TM and Th had no detectable time lag in clotting inhibition (K d = 26 nM) or PC activation (K d = 22 nM), while ATIII inhibited Th at a bimolecular rate constant = 5,200 M-1s-1 (K d <0.2 nM). A mixture of ATIII, Th and rhs-TM showed that ATIII reacted with Th slower than rhs-TM, whose presence did not affect the reaction between ATIII and Th. In a mixture of rhs-TM, ATIII and PC, the repeated addition of Th caused the repeated activation of PC; which was consistent with the Simulation based on the assumption that rhs-TM is recycled as a Th cofactor. From these results, we concluded that upon inhibition of the rhs-TM-Th complex by ATIII, rhs-TM is released to recombine with free Th and begins to activate PC, while the Th-ATIII complex does not affect rhs-TM-Th equilibrium.

Sign in / Sign up

Export Citation Format

Share Document