ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation.

While footprinting analysis of ATAC-seq data can theoretically enable investigation of transcription factor (TF) binding, the lack of a computational tool able to conduct different levels of footprinting analysis has so-far hindered the widespread application of this method. Here we present TOBIAS, a comprehensive, accurate, and fast footprinting framework enabling genome-wide investigation of TF binding dynamics for hundreds of TFs simultaneously. We validate TOBIAS using paired ATAC-seq and ChIP-seq data, and find that TOBIAS outperforms existing methods for bias correction and footprinting. As a proof-of-concept, we illustrate how TOBIAS can unveil complex TF dynamics during zygotic genome activation in both humans and mice, and propose how zygotic Dux activates cascades of TFs, binds to repeat elements and induces expression of novel genetic elements.

Reconstitution reveals how myosin-VI self-organises to generate a dynamic mechanism of membrane sculpting.

One enigma in biology is the generation, sensing and maintenance of membrane curvature. Curvature-mediating proteins have been shown to induce specific membrane shapes by direct insertion and nanoscopic scaffolding, while the cytoskeletal motors exert forces indirectly through microtubule and actin networks. It remains unclear, whether the manifold direct motorprotein-lipid interactions themselves constitute another fundamental route to remodel the membrane shape. Here we show, combining super-resolution-fluorescence microscopy and membrane-reshaping nanoparticles, that curvature-dependent lipid interactions of myosin-VI on its own, remarkably remodel the membrane geometry into dynamic spatial patterns on the nano- to micrometer scale. We propose a quantitative theoretical model that explains this dynamic membrane sculpting mechanism. The emerging route of motorprotein-lipid interactions reshaping membrane morphology by a mechanism of feedback and instability opens up hitherto unexplored avenues of membrane remodelling and links cytoskeletal motors to early events in the sequence of membrane sculpting in eukaryotic cell biology.

Conformations and membrane-driven self-organization of rodlike fd virus particles on freestanding lipid membranes.

Membrane-mediated interactions and aggregation of colloidal particles adsorbed to responsive elastic membranes are challenging problems relevant for understanding the microscopic organization and dynamics of biological membranes. We experimentally study the behavior of rodlike semiflexible fd virus particles electrostatically adsorbed to freestanding cationic lipid membranes and find that their behavior can be controlled by tuning the membrane charge and ionic strength of the surrounding medium. Three distinct interaction regimes of rodlike virus particles with responsive elastic membranes can be observed. (i) A weakly charged freestanding cationic lipid bilayer in a low ionic strength medium represents a gentle quasi-2D substrate preserving the integrity, structure, and mechanical properties of the membrane-bound semiflexible fd virus, which under these conditions is characterized by a monomer length of 884 ± 4 nm and a persistence length of 2.5 ± 0.2 µm, in perfect agreement with its properties in bulk media. (ii) An increase in the membrane charge leads to the membrane-driven collapse of fd virus particles on freestanding lipid bilayers and lipid nanotubes into compact globules. (iii) When the membrane charge is low, and the mutual electrostatic repulsion of membrane-bound virus particles is screened to a considerable degree, membrane-driven self-organization of membrane-bound fd virus particles into long linear tip-to-tip aggregates showing dynamic self-assembly/disassembly and quasi-semiflexible behavior takes place. These observations are in perfect agreement with the results of recent theoretical and simulation studies predicting that membrane-mediated interactions can control the behavior of colloidal particles adsorbed on responsive elastic membranes.

Determination of curcumin in biologically active supplements and food spices using a mesofluidic platform with fluorescence detection.

A mesofluidic platform (MP) with fluorescence detection based on a stepwise injection analysis (SWIA) was used for the determination of curcumin in biologically active supplements and food spices. The main units of the MP are a mixing chamber (MC) and an optical channel with a quartz capillary inside. The MC provides rapid and complete mixing solutions by gas bubbling. The proposed method is based on the new rapid and sensitive reaction of curcumin with a fluorescence reagent - 4-(2,3,3-trimethyl-3H-indolium-1-yl)butane-1-sulfonate (TIBS). The fluorescence intensity of TIBS is greatly quenched in the presence of curcumin in an alkaline medium. The linear range was from 1 to 10µM of curcumin, and the limit of detection, calculated as 3σ of a blank test (n=5), was found to be 0.3µM. The sample throughput was 24h(-1). The proposed method was successfully applied for the determination of curcumin in biologically active supplements and samples of food spices. The obtained data were in good agreement with those measured by a HPLC-UV method.

A Miniaturized Stepwise Injection Spectrophotometric Analyzer.

A novel micro-stepwise injection analyzer (µSWIA) has been developed for the automation and miniaturization of spectrophotometric analysis. The main unit of this device is a mixing chamber (MC) connected to the atmosphere. This part of the µSWIA provides rapid and effective homogenization of the reaction mixture components and completion of the reaction by means of gas bubbling. The µSWIA contained a rectangular labyrinth channel designed in way allowing one to eliminate bubbles by moving a solution from the MC to an optical channel. The light-emitting diode (LED) was used as a light emitter and the analytical signal was measured by a portable spectrophotometer. Fluid movement was attained via the use of a computer-controlled syringe pump. The µSWIA was successfully used for the spectrophotometric determination of cysteine in biologically active supplements and fodder by using 18-molybdo-2-phosphate heteropoly anion (18-MPA) as the reagent.

Stepwise injection spectrophotometric determination of epinephrine.

Simple, rapid and fully automated methods for the manual and automated spectrophotometric determination of epinephrine have been developed by using schemes of stepwise injection (SWIA) and sequential injection analysis (SIA) implemented in the same manifold. The determination is based on the formation of reduced form of 18-molybdodiphosphate heteropoly anion by its reaction with epinephrine. Using of the reaction vessel in the general SWIA configuration instead of a holding and reaction coil in the SIA manifold provides several essential advantages, including higher sensitivity and lower reagent consumption. The linear dependence of the analytical signal on the epinephrine concentration was preserved over the range of 1.5-30, 3.0-30, and 1.5-25µmolL(-1) by using of SWIA, SIA and spectrophotometric analysis, respectively. The relative standard deviation for the SWIA determination of 10µmolL(-1) epinephrine was 1.8% (n=10).