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 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.

The Differential Risk Factors of Physically Forced and Alcohol- or Other Drug-Enabled Sexual Assault Among University Women

2009 ◽  
Vol 24 (3) ◽  
pp. 302-321 ◽  
Author(s):  
Christopher P. Krebs ◽  
Christine H. Lindquist ◽  
Tara D. Warner ◽  
Bonnie S. Fisher ◽  
Sandra L. Martin
Keyword(s):  
High Risk ◽  
Sexual Assault ◽  
Future Research ◽  
Web Based ◽  
Campus Sexual Assault ◽  
University Women ◽  
Undergraduate Women ◽  
Reported Data ◽  
Lifestyle Activities ◽  
Very High

The Campus Sexual Assault Study examined whether undergraduate women’s victimization experiences prior to college and lifestyle activities during college were differentially associated with the type of sexual assault they experienced: physically forced sexual assault and incapacitated sexual assault. Self-reported data collected using a Web-based survey administered to more than 5,000 undergraduate women at two large public universities indicated that victimization experiences before college were differentially associated with the risk of experiencing these two types of sexual assault during college. Women who experienced forced sexual assault before college were at very high risk of experiencing forced sexual assault during college (odds ratio [OR] = 6.6). Women who experienced incapacitated sexual assault before college were also at very high risk of experiencing incapacitated sexual assault during college (OR = 3.7). Moreover, women’s substance use behaviors during college, including getting drunk and using marijuana, were strongly associated with experiencing incapacitated sexual assault but were not associated with experiencing forced sexual assault. Implications for education and prevention programs, as well as future research directions, are discussed.

scholarly journals Interaction of drugs with lipid raft membrane domains as a possible target

2020 ◽  
Vol 14 (1) ◽  
pp. 34-47
Author(s):  
Hironori Tsuchiya ◽  
Maki Mizogami
Keyword(s):  
Membrane Fluidity ◽  
Lipid Rafts ◽  
Lipid Raft ◽  
Plasma Membranes ◽  
Cellular Membrane ◽  
Membrane Lipid ◽  
Membrane Domains ◽  
Functional Protein ◽  
Lipid Complex ◽  
Physicochemical Changes

Introduction: Plasma membranes are not the homogeneous bilayers of uniformly distributed lipids but the lipid complex with laterally separated lipid raft membrane domains, which provide receptor, ion channel and enzyme proteins with a platform. The aim of this article is to review the mechanistic interaction of drugs with membrane lipid rafts and address the question whether drugs induce physicochemical changes in raft-constituting and raft-surrounding membranes. Methods: Literature searches of PubMed/MEDLINE and Google Scholar databases from 2000 to 2020 were conducted to include articles published in English in internationally recognized journals. Collected articles were independently reviewed by title, abstract and text for relevance. Results: The literature search indicated that pharmacologically diverse drugs interact with raft model membranes and cellular membrane lipid rafts. They could physicochemically modify functional protein-localizing membrane lipid rafts and the membranes surrounding such domains, affecting the raft organizational integrity with the resultant exhibition of pharmacological activity. Raft-acting drugs were characterized as ones to decrease membrane fluidity, induce liquid-ordered phase or order plasma membranes, leading to lipid raft formation; and ones to increase membrane fluidity, induce liquid-disordered phase or reduce phase transition temperature, leading to lipid raft disruption. Conclusion: Targeting lipid raft membrane domains would open a new way for drug design and development. Since angiotensin-converting enzyme 2 receptors which are a cell-specific target of and responsible for the cellular entry of novel coronavirus are localized in lipid rafts, agents that specifically disrupt the relevant rafts may be a drug against coronavirus disease 2019.

scholarly journals Effect of Nedocromil Sodium on Polymorphonuclear Leukocyte Plasma Membrane

1994 ◽  
Vol 3 (7) ◽  
pp. S21-S24 ◽  
Author(s):  
A. Kantar ◽  
N. Oggiano ◽  
P. L. Giorgi ◽  
G. V. Coppa ◽  
R. Gabbianelli ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Steady State ◽  
Membrane Fluidity ◽  
Fluorescence Anisotropy ◽  
Polymorphonuclear Leukocyte ◽  
Polymorphonuclear Leukocytes ◽  
Plasma Membranes ◽  
Nedocromil Sodium ◽  
Plasma Membrane Fluidity ◽  
Steady State Fluorescence

The effect of nedocromil sodium on the plasma membrane fluidity of polymorphonuclear leukocytes (PMNs) was investigated by measuring steady-state fluorescence anisotropy of 1-[4-trimethylammonium-phenyl]-6-phenyl- 1,3,5-hexatriene (TMA-DPH) incorporated in the membrane. Our results show that nedocromil sodium 300 μM significantly decreased membrane fluidity of PMNs. The decrease in membrane fluidity of PMNs induced by fMLP was abolished in the presence of nedocromil sodium. These data suggest that nedocromil sodium interferes with the plasma membranes of PMNs and modulates their activities.

scholarly journals Tracking Lysosome Migration within Chinese Hamster Ovary (CHO) Cells Following Exposure to Nanosecond Pulsed Electric Fields

2018 ◽  
Vol 5 (4) ◽  
pp. 103
Author(s):  
Gary Thompson ◽  
Hope Beier ◽  
Bennett Ibey
Keyword(s):  
Electric Field ◽  
Electric Fields ◽  
Mammalian Cells ◽  
Plasma Membranes ◽  
Chinese Hamster ◽  
Lateral Diffusion ◽  
Cell Swelling ◽  
Dependent Manner ◽  
Membrane Repair ◽  
Osmotic Swelling

Above a threshold electric field strength, 600 ns-duration pulsed electric field (nsPEF) exposure substantially porates and permeabilizes cellular plasma membranes in aqueous solution to many small ions. Repetitive exposures increase permeabilization to calcium ions (Ca2+) in a dosage-dependent manner. Such exposure conditions can create relatively long-lived pores that reseal after passive lateral diffusion of lipids should have closed the pores. One explanation for eventual pore resealing is active membrane repair, and an ubiquitous repair mechanism in mammalian cells is lysosome exocytosis. A previous study shows that intracellular lysosome movement halts upon a 16.2 kV/cm, 600-ns PEF exposure of a single train of 20 pulses at 5 Hz. In that study, lysosome stagnation qualitatively correlates with the presence of Ca2+ in the extracellular solution and with microtubule collapse. The present study tests the hypothesis that limitation of nsPEF-induced Ca2+ influx and colloid osmotic cell swelling permits unabated lysosome translocation in exposed cells. The results indicate that the efforts used herein to preclude Ca2+ influx and colloid osmotic swelling following nsPEF exposure did not prevent attenuation of lysosome translocation. Intracellular lysosome movement is inhibited by nsPEF exposure(s) in the presence of PEG 300-containing solution or by 20 pulses of nsPEF in the presence of extracellular calcium. The only cases with no significant decreases in lysosome movement are the sham and exposure to a single nsPEF in Ca2+-free solution.

scholarly journals A quantitative model of traffic between plasma membrane and secondary lysosomes: evaluation of inflow, lateral diffusion, and degradation.

1988 ◽  
Vol 107 (6) ◽  
pp. 2109-2115 ◽  
Author(s):  
J P Draye ◽  
P J Courtoy ◽  
J Quintart ◽  
P Baudhuin
Keyword(s):  
Plasma Membrane ◽  
Half Life ◽  
Plasma Membranes ◽  
Lateral Diffusion ◽  
Quantitative Model ◽  
Lysosomal Membrane ◽  
Membrane Area ◽  
Rat Fibroblasts ◽  
Secondary Lysosomes ◽  
Total Membrane

We present here a mathematical model that accounts for the various proportions of plasma membrane constituents occurring in the lysosomal membrane of rat fibroblasts (Draye, J.-P., J. Quintart, P. J. Courtoy, and P. Baudhuin. 1987. Eur. J. Biochem. 170: 395-403; Draye, J.-P., P. J. Courtoy, J. Quintart, and P. Baudhuin. 1987. Eur. J. Biochem. 170:405-411). It is based on contents of plasma membrane markers in purified lysosomal preparations, evaluations of their half-life in lysosomes and measurements of areas of lysosomal and plasma membranes by morphometry. In rat fibroblasts, structures labeled by a 2-h uptake of horseradish peroxidase followed by a 16-h chase (i.e., lysosomes) occupy 3% of the cellular volume and their total membrane area corresponds to 30% of the pericellular membrane area. Based on the latter values, the model predicts the rate of inflow and outflow of plasma membrane constituents into lysosomal membrane, provided their rate of degradation is known. Of the bulk of polypeptides iodinated at the cell surface, only 4% reach the lysosomes every hour, where the major part (integral of 83%) is degraded with a half-life in lysosomes of integral to 0.8 h. For specific plasma membrane constituents, this model can further account for differences in the association to the lysosomal membrane by variations in the rate either of lysosomal degradation, of inflow along the pathway from the pericellular membrane to the lysosomes, or of lateral diffusion.

Efficacy of pre-participation cardiac evaluation recommendations among athletes participating in World Athletics Championships

2019 ◽  
Vol 27 (14) ◽  
pp. 1480-1490 ◽  
Author(s):  
Örjan Dahlström ◽  
Paolo Emilio Adami ◽  
Kristina Fagher ◽  
Jenny Jacobsson ◽  
Victor Bargoria ◽  
...  
Keyword(s):  
International Association ◽  
Cost Effective ◽  
Track And Field ◽  
Cross Sectional ◽  
Middle Income ◽  
Web Based ◽  
Middle Income Countries ◽  
Cardiac Evaluation ◽  
Life Threatening ◽  
Very High

Background Athletes competing in athletics (track and field) at international level may be participating with underlying undiagnosed life-threatening cardiovascular conditions. Our objective was to analyse variations in pre-participation cardiac evaluation prevalence among athletes participating in two International Association of Athletics Federations (IAAF) World Athletics Championships, with regard to the human developmental level and global region of their home countries, as well as athletes' age category, gender, event group and medical insurance type. Design Cross-sectional web-based survey. Methods A total of 1785 athletes competing in the IAAF World Under 18 Championships Nairobi 2017 and World Championships London 2017 were invited to complete a pre-participation health questionnaire investigating the experience of a pre-participation cardiac examination. Results A total of 704 (39%) of the athletes participated. Among these, 59% (60% of women; 58% of men) reported that they had been provided at least one type of pre-participation cardiac evaluation. Athletes from very high income countries, Europe and Asia, showed a higher prevalence of at least one pre-participation cardiac evaluation. Conclusions The prevalence of pre-participation cardiac evaluation in low to middle income countries, and the African continent in particular, needs urgent attention. Furthermore, increases in evaluation prevalence should be accompanied by the development of cost-effective methods that can be adopted in all global regions.

Structure, biochemistry, and assembly of epithelial tight junctions

1987 ◽  
Vol 253 (6) ◽  
pp. C749-C758 ◽  
Author(s):  
B. Gumbiner
Keyword(s):  
Tight Junction ◽  
Tight Junctions ◽  
Plasma Membranes ◽  
Freeze Fracture ◽  
Lateral Diffusion ◽  
Junctional Complex ◽  
Epithelial Cell Layer ◽  
Dependent Cell ◽  
Freeze Fracture Electron Microscopy ◽  
Dynamic Structures

The zonula occludens (ZO), also referred to as the tight junction, forms the barrier to the diffusion of molecules and ions across the epithelial cell layer through the paracellular space. The level of electrical resistance of the paracellular pathway seems to depend on the number of strands in the ZO observed by freeze-fracture electron microscopy (EM). The ZO also forms the boundary between the compositionally distinct apical and basolateral plasma membrane domains because it is a barrier to the lateral diffusion of lipids and membrane proteins that reside in the extracytoplasmic leaflet of the membrane bilayer. In contrast to its appearance in transmission EM, the tight junction is not a fusion between the outer membrane leaflets of neighboring cells. Rather it consists of protein molecules, including the newly discovered protein ZO-1 and probably others, which bring the plasma membranes into extremely close apposition so as to occlude the extracellular space. Very little is known about the assembly of tight junctions, but several kinds of evidence suggest that they are very dynamic structures. Other elements of the epithelial junctional complex including the zonula adherens (ZA), the Ca2+-dependent cell adhesion molecule uvomorulin, or L-CAM, and actin filaments of the cytoskeleton may participate in the assembly of the ZO.

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