10 research outputs found
The Human Plasma Membrane Peripherome: Visualization and Analysis of Interactions
A major part of membrane function is conducted by proteins, both integral and
peripheral. Peripheral membrane proteins temporarily adhere to biological
membranes, either to the lipid bilayer or to integral membrane proteins with
non-covalent interactions. The aim of this study was to construct and analyze
the interactions of the human plasma membrane peripheral proteins (peripherome
hereinafter). For this purpose, we collected a dataset of peripheral proteins
of the human plasma membrane. We also collected a dataset of experimentally
verified interactions for these proteins. The interaction network created from
this dataset has been visualized using Cytoscape. We grouped the proteins based
on their subcellular location and clustered them using the MCL algorithm in
order to detect functional modules. Moreover, functional and graph theory based
analyses have been performed to assess biological features of the network.
Interaction data with drug molecules show that ~10% of peripheral membrane
proteins are targets for approved drugs, suggesting their potential
implications in disease. In conclusion, we reveal novel features and properties
regarding the protein-protein interaction network created by peripheral
proteins of the human plasma membrane.Comment: 39 pages, 5 figures, 3 supplement figures, under review in BMR
Measuring pH and Buffer Capacity in Fluids Aspirated from the Fasted Upper Gastrointestinal Tract of Healthy Adults
Purpose: The design of biorelevant conditions for in vitro evaluation of orally administered drug products is contingent on obtaining accurate values for physiologically relevant parameters such as pH, buffer capacity and bile salt concentrations in upper gastrointestinal fluids. Methods: The impact of sample handling on the measurement of pH and buffer capacity of aspirates from the upper gastrointestinal tract was evaluated, with a focus on centrifugation and freeze-thaw cycling as factors that can influence results. Since bicarbonate is a key buffer system in the fasted state and is used to represent conditions in the upper intestine in vitro, variations on sample handling were also investigated for bicarbonate-based buffers prepared in the laboratory. Results: Centrifugation and freezing significantly increase pH and decrease buffer capacity in samples obtained by aspiration from the upper gastrointestinal tract in the fasted state and in bicarbonate buffers prepared in vitro. Comparison of data suggested that the buffer system in the small intestine does not derive exclusively from bicarbonates. Conclusions: Measurement of both pH and buffer capacity immediately after aspiration are strongly recommended as “best practice” and should be adopted as the standard procedure for measuring pH and buffer capacity in aspirates from the gastrointestinal tract. Only data obtained in this way provide a valid basis for setting the physiological parameters in physiologically based pharmacokinetic models
Measuring pH and Buffer Capacity in Fluids Aspirated from the Fasted Upper Gastrointestinal Tract of Healthy Adults
Purpose: The design of biorelevant conditions for in vitro evaluation of orally administered drug products is contingent on obtaining accurate values for physiologically relevant parameters such as pH, buffer capacity and bile salt concentrations in upper gastrointestinal fluids. Methods: The impact of sample handling on the measurement of pH and buffer capacity of aspirates from the upper gastrointestinal tract was evaluated, with a focus on centrifugation and freeze-thaw cycling as factors that can influence results. Since bicarbonate is a key buffer system in the fasted state and is used to represent conditions in the upper intestine in vitro, variations on sample handling were also investigated for bicarbonate-based buffers prepared in the laboratory. Results: Centrifugation and freezing significantly increase pH and decrease buffer capacity in samples obtained by aspiration from the upper gastrointestinal tract in the fasted state and in bicarbonate buffers prepared in vitro. Comparison of data suggested that the buffer system in the small intestine does not derive exclusively from bicarbonates. Conclusions: Measurement of both pH and buffer capacity immediately after aspiration are strongly recommended as “best practice” and should be adopted as the standard procedure for measuring pH and buffer capacity in aspirates from the gastrointestinal tract. Only data obtained in this way provide a valid basis for setting the physiological parameters in physiologically based pharmacokinetic models. © 2020, Springer Science+Business Media, LLC, part of Springer Nature