Silver ions as EM marker of congo red ligation sites in amyloids and amyloid-like aggregates

Congo red (CR) which is known to act as selective amyloid ligand may when binds to these protein forms reflect their internal molecular structure. The disclosure by EM of sites binding the dye and their distribution in amyloids and amyloid-like aggregates formed in vitro is the focus of our work. In order to produce the required contrast, CR has been indirectly combined with metal via including by intercalation of Titan yellow (TY) which exhibits relatively strong affinity for silver ions. The resulting combined ligand retains its ability to bind to proteins which it owes to CR and can easily be detected in EM studies thanks to TY less active in penetration to proteins. We have found however that in protein aggregates where unfolding is stabilized by aggregation and therefore irreversible, TY alone may serve as both ligand and metal carrier.The formation of ordered structures in amyloids were studied using IgG light chains with amyloidogenic properties, converted into amyloids through shaking. The resulting EM images were subjected to interpretation on the basis of the authors’ earlier research into the CR/light chain complexation process. Results indicate that dimeric light chains, which are the subject of our study, produce amyloids or amyloid-like complexes with chain-like properties and strong helicalization tendencies. Cursory analysis suggests that edge polypeptide loops belonging to unstable light chains form intermolecular bridges which promote creation of loose gel deposits, or are otherwise engaged in swapping processes leading to higher structural ordering.</jats:p

Even-odd alternative dispersions and beyond. Part II. Noninertial and inertial particles, and, astrophysical chirality analogy

Particle transports in carriers with even-odd alternating dispersions (introduced in Part I) are investigated. For the third-order dispersion as in Korteweg-de-Vries (KdV), such alternating dispersion has the effects of not only regularizing the velocity from forming shock singularity (thus the attenuation of particle clustering strength) but also symmetrizing the oscillations (thus the corresponding skewness of the particle densities), among others, as demonstrated numerically. The analogy of such dispersion effects and consequences (on particle transports in particular) with those of helicity in Burgers turbulence, addressed in the context of astrophysics and cosmology, is made for illumination and promoting models. Both dispersion and helicity regularize the respective systems, and both are shown to be transferred by the drag to the flows of the respective inertial particles carried by the latter and to similarly affect the particle clustering. A reward from studying particle transports is the understanding of the (asymptotic) $k^0$-scaling (equipartition among the wavenumbers, $k$s), before large-$k$ exponential decay, of the power spectrum of KdV solitons [resulting in the more general statement (valid beyond the KdV soliton and Burgers shock) that "a (one-dimensional) soliton is the derivative of a classical shock, just like the Dirac delta is the derivative of a step function"], motivated by the explanation of the the same scaling law of the particle densities as the apparent approximation of the Dirac deltas; while, the "shocliton" from the even-odd alternating dispersion in aKdV appears to be, indeed, $shock \oplus soliton$, accordingly the decomposition of the averaged odd-mode spectrum, from sinusoidal initial field, into a $k^{-2}$ part for the shock and a $k^0$-scaling part for the solitonic pulses, only the latter being contained in the averaged even-mode spectrum.Comment: an important statement, correctly stated in the Abstract, was stated oppositely in the main text; now corrected together with some other minor polishment. Sister to https://doi.org/10.48550/arXiv.2302.1202

Low threshold random lasing from phase separated optical fibers.

In this thesis, a low threshold novel random fiber laser, integrating a passive optical fiber with a phase separated aluminosilicate core – silica cladding as the feedback medium, is proposed and presented. The core exhibits greatly enhanced Rayleigh scattering, therefore requiring a significantly reduced length of scattering fiber (4 m) for lasing. The enhanced Rayleigh scattering was verified through measurements and a new figure of merit called effective power reflectivity was also developed to quantify random feedback. With a Yb-doped fiber as the gain medium, the fiber laser operates at 1050 nm with low threshold power, with a tractable lasing wavelength and maximum linewidth, and possesses an output that can be amplified through conventional means. Furthermore, the laser was found to have a high degree of spatial coherence, spectral broadening with increasing input power, and temporal spectral variation. The random lasing action was confirmed both by the use of RF beat spectra measurements and the trends in the Lévy exponent α obtained from the statistics of spectral intensity variation. Cutback experiments carried out shed light on the evolution of lasing behavior with P-SOF length and the impact of feedback on the lasing behavior. The minimum length of P-SOF required for maximum Rayleigh-distributed feedback was also determined to be ~ 2.5 m. This facile setup and results herein pave the way for further study and applications based on low threshold and compact random fiber lasers

Passive thermal management in high-power fiber laser systems

Parasitic and catastrophic thermal effects serve as the limiting factors for further power scaling in high-power fiber lasers. Among the different thermal energy generation processes, quantum defect (QD) heating ultimately serves as the dominant heat source in an optimized system. In a typical laser system, a positive QD gives net heating because the pump photon energy is higher than that of the signal. To reduce quantum defect heating, two approaches are investigated, both theoretically and experimentally. Since Yb-doped fiber lasers give the highest output power compared to any other fiber laser systems, the discussions herein mainly focus on Yb-doped fiber laser systems. The first approach is to reduce the QD heating by bringing the signal wavelength closer to the pumping wavelength. This requires exploring new host glasses for Yb3+ including fluorosilicates and phosphosilicates, so that efficient optical gain at shorter wavelengths can be achieved. Both low-power (< 1W pump power) linear cavity lasers and high-power (20 W pump power) amplifiers are demonstrated when pumping at ~975 nm. The former exhibited nearly 70% slope efficiency at 985.7 nm while the latter had an 87.4 % slope efficiency with respect to absorbed pump power when operating at 1005 nm. Theoretical models based on rate equations were built and the experimental results agree well with the simulations. Calculations are also performed to explore improved fiber designs and the possibility of a double-end pumping scheme. The second approach is to introduce a “cooling” mechanism so that the overall QD heating is reduced. To do so, a negative contribution to the QD is added via a second pumping wavelength positioned to the red side of the lasing wavelength (anti-Stokes pump). Since the balancing of the thermal energy is introduced through excitation of the system at two wavelengths, such a system is named excitation-balanced fiber laser or amplifier. Demonstrated first is a laser operating in a pulsed regime. The experimental results indicate that anti-Stokes pumping can effectively contribute to stimulated emission in a solid, resulting in a form of self-cooling. An FDTD model is built to further understand and optimize the system. Next, modeling of a high-energy excitation-balanced pulse amplifier is performed. Results indicate that a heat-free mJ-level pulse amplifier is possible. The influences from several input parameters, such as pump power, pump pulse width, and repetition rate are also discussed in detail, providing valuable guidance for future design and experiments. Last but not the least, since thermal energy can also be generated via nonradiative processes, a testing platform based on Brillouin scattering is proposed to quantify those sources of heating. The functionality of the platform is confirmed by testing a commercial Yb-doped fiber, and a few demonstrations of anti-Stokes fluorescence cooling are made in nanoparticle doped fiber. Such a flatform will be useful for optimizing glass quality. Finally, a brief conclusion is provided, and several future works are proposed.Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2022-11-11 without embargo termsThe student, Nanjie Yu, accepted the attached license on 2022-03-20 at 12:27.The student, Nanjie Yu, submitted this Dissertation for approval on 2022-03-20 at 12:34.This Dissertation was approved for publication on 2022-03-24 at 15:16.DSpace SAF Submission Ingestion Package generated from Vireo submission #17541 on 2022-11-11 at 13:04:3

Non-covalent interactions in organotin(IV) derivatives of 5,7-ditertbutyl- and 5,7-diphenyl-1,2,4-triazolo[1,5-a]pyrimidine as recognition motifs in crystalline self- assembly and their in vitro antistaphylococcal activity

Non-covalent interactions are known to play a key role in biological compounds due to their stabilization of the tertiary and quaternary structure of proteins [1]. Ligands similar to purine rings, such as triazolo pyrimidine ones, are very versatile in their interactions with metals and can act as model systems for natural bio-inorganic compounds [2]. A considerable series (twelve novel compounds are reported) of 5,7-ditertbutyl-1,2,4-triazolo[1,5-a]pyrimidine (dbtp) and 5,7-diphenyl- 1,2,4-triazolo[1,5-a]pyrimidine (dptp) were synthesized and investigated by FT-IR and 119Sn M\uf6ssbauer in the solid state and by 1H and 13C NMR spectroscopy, in solution [3]. The X-ray crystal and molecular structures of Et2SnCl2(dbtp)2 and Ph2SnCl2(EtOH)2(dptp)2 were described, in this latter pyrimidine molecules are not directly bound to the metal center but strictly H-bonded, through N(3), to the -OH group of the ethanol moieties. The network of hydrogen bonding and aromatic interactions involving pyrimidine and phenyl rings in both complexes drives their self-assembly. Noncovalent interactions involving aromatic rings are key processes in both chemical and biological recognition, contributing to overall complex stability and forming recognition motifs. It is noteworthy that in Ph2SnCl2(EtOH)2(dptp)2 \u3c0\u2013\u3c0 stacking interactions between pairs of antiparallel triazolopyrimidine rings mimick basepair interactions physiologically occurring in DNA (Fig.1). M\uf6ssbauer spectra suggest for Et2SnCl2(dbtp)2 a distorted octahedral structure, with C-Sn-C bond angles lower than 180\ub0. The estimated angle for Et2SnCl2(dbtp)2 is virtually identical to that determined by X-ray diffraction. Ph2SnCl2(EtOH)2(dptp)2 is characterized by an essentially linear C-Sn-C fragment according to the X-ray all-trans structure. The compounds were screened for their in vitro antibacterial activity on a group of reference staphylococcal strains susceptible or resistant to methicillin and against two reference Gramnegative pathogens [4] . We tested the biological activity of all the specimen against a group of staphylococcal reference strains (S. aureus ATCC 25923, S. aureus ATCC 29213, methicillin resistant S. aureus 43866 and S. epidermidis RP62A) along with Gram-negative pathogens (P. aeruginosa ATCC9027 and E. coli ATCC25922). Ph2SnCl2(EtOH)2(dptp)2 showed good antibacterial activity with a MIC value of 5 \u3bcg mL-1 against S. aureus ATCC29213 and also resulted active against methicillin resistant S. epidermidis RP62A

Influence of Tyrosine-Derived Moieties and Drying Conditions on the Formation of Helices in Gelatin

The single and triple helical organization of protein chains strongly influences the mechanical properties of gelatin-based materials. A chemical method for obtaining different degrees of helical organization in gelatin is covalent functionalization, while a physical method for achieving the same goal is the variation of the drying conditions of gelatin solutions. Here we explored how the introduction of desaminotyrosine (DAT) and desaminotyrosyl tyrosine (DATT) linked to lysine residues of gelatin influenced the kinetics and thermodynamic equilibrium of the helicalization process of single and triple helices following different drying conditions. Drying at a temperature above the helix-to-coil transition temperature of gelatin (T > Tc, called vshort) generally resulted in gelatins with relatively lower triple helical content (Xc,t = 1−2%) than lower temperature drying (T Tc, called vlong) (Xc,t = 8−10%), where the DAT(T) functional groups generally disrupted helix formation. While different helical contents affected the thermal transition temperatures only slightly, the mechanical properties were strongly affected for swollen hydrogels (E = 4−13 kPa for samples treated by vlong and E = 120−700 kPa for samples treated by vshort). This study shows that side group functionalization and different drying conditions are viable options to control the helicalization and macroscopic properties of gelatin-based materials

Salt-induced shape-memory effect in gelatin-based hydrogels

Hydrophilic biopolymers display a strong tendency for self-organization into stable secondary, tertiary, and quaternary structures in aqueous environments. These structures are sensitive to changes in external conditions, such as temperature, pH or ions/salts, which may lead to molecular and/or macroscopic transitions. Here, we report on biopolymer-based stimuli-sensitive switchable matrices showing a shape-memory function as an output being alternatively switched by two different input signals, such as environmental changes in salt concentration or temperature. This was realized by implementing a shape-memory function in hydrogels based on the coil-to-helix transition of protein chains in gelatin-based networks. The hydrogels exhibited mechanical properties similar to that of soft tissue (storage modulus G' = 1-100 kPa) and high swelling capabilities (Q = 1000-3000 vol %). In these gelatin-based networks, the covalent netpoints defined the permanent shape while after deformation helicalization of the gelatin acted as reversible stimuli-sensitive switches providing additional crosslinks capable of fixing the deformed temporary shape. By using either chaotropic salts to suppress gelatin helicalization or kosmotropic salts to support conformational changes of gelatin toward a helical orientation, these additional crosslinks could be cleaved or formed. In bending experiments, the strain fixity (R-f) and strain recovery ratios (R-r) were determined. While R-f ranged from 65 to 95% and was depending on the network composition, R-r were independent of the hydrogel composition with values about 100%. In addition, R-f and R-r were independent of the type of chaotropic salt that was used in this study, showing equal R-f and R-r, values for MgCl2, NaSCN, and Mg(SCN)(2)

Influence of tyrosine-derived moieties and drying conditions on the formation of helices in gelatin

The single and triple helical organization of protein chains strongly influences the mechanical properties of gelatin-based materials. A chemical method for obtaining different degrees of helical organization in gelatin is covalent functionalization, while a physical method for achieving the same goal is the variation of the drying conditions of gelatin solutions. Here we explored how the introduction of desaminotyrosine (DAT) and desaminotyrosyl tyrosine (DATT) linked to lysine residues of gelatin influenced the kinetics and thermodynamic equilibrium of the helicalization process of single and triple helices following different drying conditions. Drying at a temperature above. the helix-to-coil transition temperature of gelatin (T > T-c, called nu(short)) generally resulted in gelatins with relatively lower triple helical content (X-c,X-t = 1-2%) than lower temperature drying (T < T-c, called nu(long)) (X-c,X-t = 8-10%), where the DAT(T) functional groups generally disrupted helix formation. While different helical contents affected the thermal transition temperatures only slightly, the mechanical properties were strongly affected for swollen hydrogels (E = 4-13 kPa for samples treated by nu(long) and E = 120-700 kPa for samples treated by nu(short)). This study shows that side group functionalization and different drying conditions are viable options to control the helicalization and macroscopic properties of gelatin-based materials

Structure of the alpha-homo-DNA:RNA duplex and the Function of Twist and Slide To Catalogue Nucleic Acid Duplexes

High-resolution NMR studies of an alpha-homo-DNA:RNA duplex reveal the formation of a right-handed parallel-oriented helix. It differs significantly from a standard A- or B-type helix by a small twist value (26.2 degrees ), which leads to a helical pitch of 13.7 base pairs per helical turn, a negative inclination (-1.78 A) and a large x displacement (5.90 A). The rise (3.4 A) is similar to that found in B-DNA. The solution of this new helix structure has stimulated us to develop a mathematical and geometrical model based on slide and twist parameters to describe nucleic acid duplexes. All existing duplexes can be positioned within this landscape, which can be used to understand the helicalization process.status: publishe