GNNQQNY: Methodology for biophysical and structural understanding of aggregation

GNNQQNY sequence offers crucial information about the formation and structure of an amyloid fibril. In this study, we demonstrate a reproducible solubilisation protocol where the reduction of pH to 2.0 resulted in the generation of GNNQQNY monomers. The subsequent ultracentrifugation step removes the residual insoluble peptide from the homogeneous solution. This procedure ensures and allows the peptides to remain monomers till their aggregation is triggered by adjusting the pH to 7.2. The aggregation kinetics analysis showed a distinct lag-phase that is concentration-dependent, indicating nucleation-dependent aggregation kinetics. Nucleation kinetics analysis suggested a critical nucleus of size ~7 monomers at physiological conditions. The formed nucleus acts as a template for further self-assembly leading to the formation of highly ordered amyloid fibrils. These findings suggest that the proposed solubilisation protocol provides the basis for understanding the kinetics and thermodynamics of amyloid nucleation and elongation in GNNQQNY sequences. This procedure can also be used for solubilising such small amyloidogenic sequences for their biophysical studies.

Hadrons as QCD Bound States

Bound state perturbation theory is well established for QED atoms. Today the hyperfine splitting of Positronium is known to 𝒪 (α7 log α). Whereas standard expansions of scattering amplitudes start from free states, bound states are expanded around eigenstates of the Hamiltonian including a binding potential. The eigenstate wave functions have all powers of α, requiring a choice in the ordering of the perturbative expansion. Temporal (A0 = 0) gauge permits an expansion starting from valence Fock states, bound by their instantaneous gauge field. This formulation is applicable in any frame and seems promising even for hadrons in QCD. The 𝒪(αs0) confining potential is determined (up to a universal scale) by a homogeneous solution of Gauss’ law.

Assessment of computer vision methods for motion tracking of planar mechanisms

One of the main challenges on the use of planar mechanisms is to verify and monitor that the trajectories described by the mechanism correspond to those originally required. However, very few research studies have focused on tracking and monitoring the motion of target points located on the mechanisms during operation conditions. In this paper, a comparative study to evaluate the performance of several computer vision methods (CVMs) when used in motion tracking of planar mechanisms is presented. The aim is to compare and identify the best CVM, in terms of precision, speed, low cost, and computational performance, to track the movement of planar mechanisms. For this purpose, a case study corresponding to a planar four-bar mechanism is selected and analysed. The results show that the vision methods based on the homogeneous and non-homogeneous solution of the camera calibration matrix are a technological alternative for monitoring motion trajectories of planar mechanisms.

Sufficient Turing instability conditions for the Schnakenberg system

A classical reaction-diffusion system, the Schnakenberg system, is under consideration in a bounded domain $\Omega\subset\mathbb{R}^m$ with Neumann boundary conditions. We study diffusion-driven instability of a stationary spatially homogeneous solution of this system, also called the Turing instability, which arises when the diffusion coefficient $d$ changes. An analytical description of the region of necessary and sufficient conditions for the Turing instability in the parameter plane is obtained by analyzing the linearized system in diffusionless and diffusion approximations. It is shown that one of the boundaries of the region of necessary conditions is an envelope of the family of curves that bound the region of sufficient conditions. Moreover, the intersection points of two consecutive curves of this family lie on a straight line whose slope depends on the eigenvalues of the Laplace operator and does not depend on the diffusion coefficient. We find an analytical expression for the critical diffusion coefficient at which the stability of the equilibrium position of the system is lost. We derive conditions under which the set of wavenumbers corresponding to neutral stability modes is countable, finite, or empty. It is shown that the semiaxis $d>1$ can be represented as a countable union of half-intervals with split points expressed in terms of the eigenvalues of the Laplace operator; each half-interval is characterized by the minimum wavenumber of loss of stability.

A Self-Immolative Molecular Beacon for Amplified Nucleic Acid Detection

Fluorogenic hybridization probes allow the detection of RNA and DNA sequences in homogeneous solution. Typically, one target molecule is activating the fluorescence of a single probe molecule. This limits the sensitivity of nucleic acid detection. Herein, we report a self-immolative Molecular Beacon (iMB), which escapes the one-target-one-probe dogma. The iMB probe includes a photoreductively cleavable N-alkylpicolinium (NAP) linkage within the loop region. A fluorophore at the 5'-end serves, on the one hand, as a reporter group and, on the other hand, as a photosensitizer of a NAP-linker cleavage reaction. In the absence of a target, the iMB adopts a hairpin shape. Quencher proups prevent photo-induced cleavage. The iMB opens upon hybridization with target, and both fluorescent emission as well as photo-inductive cleavage of the NAP-linker can occur. In contrast to previous chemical amplification probes, iMBs are unimolecular. Cleavage leads to products that have lower target affinity than the probes before reaction. Aided by catalysis, the method allowed the detection of 5 pM RNA target within 100 min. <br>

A Self-Immolative Molecular Beacon for Amplified Nucleic Acid Detection

Fluorogenic hybridization probes allow the detection of RNA and DNA sequences in homogeneous solution. Typically, one target molecule is activating the fluorescence of a single probe molecule. This limits the sensitivity of nucleic acid detection. Herein, we report a self-immolative Molecular Beacon (iMB), which escapes the one-target-one-probe dogma. The iMB probe includes a photoreductively cleavable N-alkylpicolinium (NAP) linkage within the loop region. A fluorophore at the 5'-end serves, on the one hand, as a reporter group and, on the other hand, as a photosensitizer of a NAP-linker cleavage reaction. In the absence of a target, the iMB adopts a hairpin shape. Quencher proups prevent photo-induced cleavage. The iMB opens upon hybridization with target, and both fluorescent emission as well as photo-inductive cleavage of the NAP-linker can occur. In contrast to previous chemical amplification probes, iMBs are unimolecular. Cleavage leads to products that have lower target affinity than the probes before reaction. Aided by catalysis, the method allowed the detection of 5 pM RNA target within 100 min. <br>

A Comparison of Commercially Available Screen-Printed Electrodes for Electrogenerated Chemiluminescence Applications

We examined a series of commercially available screen-printed electrodes (SPEs) for their suitability for electrochemical and electrogenerated chemiluminescence (ECL) detection systems. Using cyclic voltammetry with both a homogeneous solution-based and a heterogeneous bead-based ECL assay format, the most intense ECL signals were observed from unmodified carbon-based SPEs. Three commercially available varieties were tested, with Zensor outperforming DropSens and Kanichi in terms of sensitivity. The incorporation of nanomaterials in the electrode did not significantly enhance the ECL intensity under the conditions used in this evaluation (such as gold nanoparticles 19%, carbon nanotubes 45%, carbon nanofibers 21%, graphene 48%, and ordered mesoporous carbon 21% compared to the ECL intensity of unmodified Zensor carbon electrode). Platinum and gold SPEs exhibited poor relative ECL intensities (16% and 10%) when compared to carbonaceous materials, due to their high rates of surface oxide formation and inefficient oxidation of tri-n-propylamine (TPrA). However, the ECL signal at platinum electrodes can be increased ∼3-fold with the addition of a surfactant, which enhanced TPrA oxidation due to increasing the hydrophobicity of the electrode surface. Our results also demonstrate that each SPE should only be used once, as we observed a significant change in ECL intensity over repeated CV scans and SPEs cannot be mechanically polished to refresh the electrode surface.