Genome assembly and annotation for red clover (Trifolium pratense; Fabaceae).

Premise Of The Study: Red clover (Trifolium pratense) is an important forage plant from the legume family with great importance in agronomy and livestock nourishment. Nevertheless, assembling its medium-sized genome presents a challenge, given current hardware and software possibilities. Next-generation sequencing technologies enable us to generate large amounts of sequence data at low cost.

Eigenmobilities in background electrolytes for CZE. V. Intensity (amplitudes) of system peaks.

We present a mathematical model of CZE based on the concept of eigenmobilities - the eigenvalues of matrix M tied to the linearized governing equations of electromigration, and the spectral decomposition of matrix M into matrices of amplitudes P(j). Any peak in an electropherogram, regardless of whether it is an analyte peak or a system peak (system zone), is matched with its matrix P(j). This enables calculation of the peak parameters, such as the transfer ratio and the molar conductivity detection response (which give the indirect detection signal and the conductivity detection signal, respectively), when the initial disturbance caused by the injection of the sample is known.

Simul 5 - free dynamic simulator of electrophoresis.

We introduce the mathematical model of electromigration of electrolytes in free solution together with free software Simul, version 5, designed for simulation of electrophoresis. The mathematical model is based on principles of mass conservation, acid-base equilibria, and electroneutrality. It accounts for any number of multivalent electrolytes or ampholytes and yields a complete picture about dynamics of electromigration and diffusion in the separation channel.

Oscillating electrolytes.

Chemical oscillations are driven by the gradient of the chemical potential so that they can appear in systems where the substances are not in chemical equilibrium. We show that under the influence of the electric field, concentrations of electrically charged substances in solutions can oscillate even if the system is in chemical equilibrium. The driving force here is not the gradient of the chemical potential but rather the gradient of the electric potential.

Conductivity detection in capillary zone electrophoresis: inspection by PeakMaster.

A simple rule stating that the signal in conductivity detection in capillary zone electrophoresis is proportional to the difference between the analyte mobility and mobility of the background electrolyte (BGE) co-ion is valid only for systems with fully ionized electrolytes. In zone electrophoresis systems with weak electrolytes both conductivity signal and electromigration dispersion of analyte peaks depend on the conductivity and pH effects. This allows optimization of the composition of BGEs to give a good conductivity signal of analytes while still keeping electromigration dispersion near zero, regardless of the injected amount of sample.

Eigenmobilities in background electrolytes for capillary zone electrophoresis: IV. Computer program PeakMaster.

We are introducing a computer implementation of the mathematical model of zone electrophoresis (CZE) described in Stedry, M., Jaros, M., Hruska, V.

Eigenmobilities in background electrolytes for capillary zone electrophoresis: III. Linear theory of electromigration.

A mathematical model of capillary zone electrophoresis (CZE) based on the conception of eigenmobilities, which are the eigenvalues of a matrix M tied to the linearized governing equations is presented. The model considers CZE systems, where constituents, either analytes or components of the background electrolyte (BGE), are weak electrolytes--acids, bases, or ampholytes. There is no restriction on the number of components nor on the valence of the constituents nor on pH of the BGE.

Detection of molecular interactions at membrane surfaces through colloid phase transitions.

The molecular architecture of-and biochemical processes within--cell membranes play important roles in all living organisms, with many drugs and infectious disease agents targeting membranes. Experimental studies of biochemical reactions on membrane surfaces are challenging, as they require a membrane environment that is fluid (like cell membranes) but nevertheless allows for the efficient detection and characterization of molecular interactions. One approach uses lipid membranes supported on solid substrates such as silica or polymers: although the membrane is trapped near the solid interface, it retains natural fluidity and biological functionality and can be implanted with membrane proteins for functional studies.

Eigenmobilities in background electrolytes for capillary zone electrophoresis: II. Eigenpeaks in univalent weak electrolytes.

We analyze in detail a mathematical model of capillary zone electrophoresis (CZE) based on the conception of eigenmobilities, which are eigenvalues of the matrix tied to the linearized continuity equations. Our model considers CZE systems, where constituents are weak electrolytes and where pH of the background electrolyte may reach the full range from 0 to 14. Both hydrogen and hydroxide ions are taken into account in relations for conductivity and electroneutrality.

Optimization of background electrolytes for capillary electrophoresis: II. Computer simulation and comparison with experiments.

A mathematical and computational model described in the previous paper (Gas, B., Coufal, P., Jaros, M.

Eigenmobilities in background electrolytes for capillary zone electrophoresis. I. System eigenpeaks and resonance in systems with strong electrolytes.

A background electrolyte system for capillary zone electrophoresis which is composed of three strong univalent ionic constituents is investigated. The ion 1 is considered as a counter-ion and two ions, 2 and 3, are considered as co-ions in relation to the analyte ion 4. We investigate the linearized model of electromigration in such a system and calculate the eigenvalues of a corresponding matrix.