Well Plate Maker: a user-friendly randomized block design application to limit batch effects in large-scale biomedical studies

Summary Many factors can influence results in clinical research, in particular bias in the distribution of samples prior to biochemical preparation. Well Plate Maker is a user-friendly application to design single- or multiple-well plate assays. It allows multiple group experiments to be randomized and therefore helps to reduce possible batch effects. Although primarily fathered to optimize the design of clinical sample analysis by high throughput mass spectrometry (e.g. proteomics or metabolomics), it includes multiple options to limit edge-of-plate effects, to incorporate control samples or to limit cross-contamination. It thus fits the constraints of many experimental fields. Availability and implementation Well Plate Maker is implemented in R and available at Bioconductor repository (https://bioconductor.org/packages/wpm) under the open source Artistic 2.0 license. In addition to classical scripting, it can be used through a graphical user interface, developed with Shiny technology.

«Biological and bioorganic chemistry». 2 Vol. Vol. 1 «Molecular organization of living matter. Metabolisms and bioenergetics». Vol. 2 «Bіоchemical aspects of molecular biology and intercellular communications» / L. I. Ostapchenko, V. K. Rybalchenko

The article reviews the textbook «Biological and Bioorganic Chemistry», intended for students of biological specialties. The textbook examines the main provisions of static and dynamic biochemistry – the science of the pathways and mechanisms of biochemical processes occurring in the cell. Not only the general characteristics of metabolic activity, but also sections related to the regulation of metabolism and the physiological functions of cells are presented. The mechanisms of global metabolic regulation, which are characteristic for all living organisms, are disclosed. The textbook is intended for students of higher educational institutions receiving education in the areas of «Biology», «Ecology», «Chemical technology and biotechnology»; specialties «Biology», «Physiology», «Microbiology», «Biotechnology», «Molecular biology», «Bioecology». It is of interest for specialists, researchers, postgraduates and doctoral students who need basic biochemical preparation.

Non-vesicular transfer of membrane proteins from nanoparticles to lipid bilayers

Discoidal lipoproteins are a novel class of nanoparticles for studying membrane proteins (MPs) in a soluble, native lipid environment, using assays that have not been traditionally applied to transmembrane proteins. Here, we report the successful delivery of an ion channel from these particles, called nanoscale apolipoprotein-bound bilayers (NABBs), to a distinct, continuous lipid bilayer that will allow both ensemble assays, made possible by the soluble NABB platform, and single-molecule assays, to be performed from the same biochemical preparation. We optimized the incorporation and verified the homogeneity of NABBs containing a prototypical potassium channel, KcsA. We also evaluated the transfer of KcsA from the NABBs to lipid bilayers using single-channel electrophysiology and found that the functional properties of the channel remained intact. NABBs containing KcsA were stable, homogeneous, and able to spontaneously deliver the channel to black lipid membranes without measurably affecting the electrical properties of the bilayer. Our results are the first to demonstrate the transfer of a MP from NABBs to a different lipid bilayer without involving vesicle fusion.