Biophysica, Volume 4, Issue 3 (September 2024) – 7 articles

This study investigates the formation and impact of Endogenous Quasi-Pathogens (EQPs) within cellular environments, focusing on the role of Endogenous Smart Medicine (ESM) as a therapeutic intervention. This work elucidates how induced vibrations facilitate new molecular and atomic connections between adjacent cells, leading to endobiotic bond formation and significantly altered DNA behavior. These vibrations, which dominate cellular processes, induce both temporary and permanent changes in cellular dynamics. The resulting increase in extracellular impedance triggers the emergence of new EQP sources, potentially initiating divergent pathological cycles. Cells experiencing moderate impedance changes are classified as benign, while those with substantial alterations are considered malignant. This study highlights the medical diagnostic implications of EQPs and positions ESM as a precise method for modulating cellular impedance, reducing the effects of EQPs, and potentially treating diseases where disruptions in cellular dynamics and stiffness are critical. Additionally, the integration of ChronoBit Storage (CBS) within ESM introduces a novel energy management mechanism, enhancing therapeutic precision by synchronizing energy distribution with cellular needs. The ChronoVital Index (CVI), a temporal model for assessing time dynamics across biological systems from individual cells to whole organs further refines this approach. By advancing the CVI and CBS, this research paves the way for more sophisticated therapeutic strategies, offering promising applications in the fields of disease management and cellular restoration within the framework of Endogenous Smart Medicine. Full article

Experiments to measure a single molecule/particle, i.e., an individual molecule/particle, at room temperature or under physiological conditions without immobilization—for example, on a surface or without significant hydrodynamic flow—have so far failed. This failure has given impetus to the underlying theory of Brownian molecular motion towards its stochastics due to diffusion. Quantifying the thermodynamic jitter of molecules/particles inspires many and forms the theoretical basis of single-molecule/single-particle biophysics and biochemistry. For the first time, our simulation results for a live cell (cytoplasm) show that the tracks of individual single molecules are localized in Brownian motion, while there is fanning out in fractal diffusion (anomalous diffusion). Full article

This study presents a quantum well model using the transfer matrix technique to analyze the charge transfer characteristics of nanostructure sequences in both DNA and superlattices. The unconfined state, or unbound state, above the quantum well is used to investigate carrier behaviors in a semiconductor nanostructure. These analytical approaches can be extended to enhance the understanding of charge transfer in DNA nanostructures with periodic and aperiodic sequences. Experimental validation was conducted through photoreflectance spectroscopy on nanostructures within the semiconductor superlattices. Furthermore, the study’s findings were compared with earlier research by Li et al. on the thermoelectric effect and its dependence on molecular length and sequences in single DNA molecules. The results showed agreement, offering novel insights into charge transfer and transport in DNA nanostructures across various sequence types. Full article

Bone minerals may be more complex than the prevailing opinion suggests. Understanding its biomaterial properties in health and disease may address fundamental geo/biomorphological ambiguities recurrent within its calcified cancellous hierarchy of macro-, micro-, and nano-skeletal networks. (i) There is evidence that the outer mineral macroskeleton of interconnected trabeculae (150 µm diameter) is modulated according to axes of tensile stress by permeating arrays of periosteal Sharpey’s fibres (collagen type III/VI, 5–25 µm thick) studded with tenascin organiser protein. (ii) Its substructural mineral microskeleton is a reticulation of bridged and deformable calcium phosphate/carbonate microspheres (about 1 µm diameter). These organically enshrouded (e.g., bone sialoprotein, osteocalcin, osteopontin) objects, configured by the adhesive organiser protein fibronectin and tempered by trace elements (e.g., Si, Mg, Fe, Al), display differential histochemistry (e.g., acid phosphatase, carbonic anhydrase) and anomalous traits (tetracycline binding, gram-positive microbial staining and nucleic acid staining affinity). The calcified microspheres are intracellular fabrications of osteocyte cohorts developed within “switched on” Golgi cisternae prior to aggregation at the extracellular calcification front in chains and looped assemblies. (iii) Within each microsphere, a less dense centre is encircled by a mineral nanoskeleton of beaded filaments (5 nm in diameter) transmutable in electron density, with a trait for lateral fusion into ladder-like struts, stays and senescent fenestrated plates, constituting domains of microparticle slip and crystal fracture. The evidence suggests a bone mineral biosystem of integrated complexity within which a particulate assemblage at the animate: inanimate calcification front resembles a colonial construct of prokaryote-like, Golgi-fabricated objects calcified with phosphate and harbouring a resident biochemistry. A self-contained “Petrified Microbiome” is proposed to be orchestrated according to a biodynamic primordial paradigm. Full article

Aqueous two-phase systems (ATPSs) are formed when two nonionic polymers, or a single polymer and salt, are mixed in water above a specific concentration, resulting in the emergence of phase separation and the formation of two immiscible aqueous phases. The solvent properties of the aqueous media within the phases of ATPSs rely on the specific composition of the co-solutes and the arrangement of the hydrogen bond network within each phase. Here, we investigate the anion effect of various sodium salts on the enhancement or destabilization of polyethylene glycol (PEG)–salt ATPS formation. Relatively small changes in ATPS ionic composition were shown to result in significant changes in solute partitioning. Additionally, we previously established that the arrangement of hydrogen bonds within the coexisting phases of ATPSs is different, as evidenced by Attenuated Total Reflection—Fourier Transform Infrared (ATR-FTIR) spectroscopic analysis of OH-stretch bands. The hydrogen bond arrangement was shown to abruptly change at concentrations below the threshold of macroscopic phase separation in the ATPSs. Using dynamic light scattering (DLS), we observed a correlation between these abrupt changes in H-bond arrangement and the detection of agglomerate formation in both polymer–polymer and polymer–salt systems. Full article

Herein, we propose an analytical approach based on intermolecular fluorescent resonant energy transfer (FRET) pairs for the visualization of specific enzyme activity in model biomembranes and in living cells. Cell visualizations with fluorescent confocal laser microscopy usually rely on fluorescent probes, such as Fluorescein isothiocyanate (FITC), Alexa488, Tetramethylrhodamine isothiocyanate (TRITC) and many others. However, for more specific tasks, such as the detection of certain enzymatic activity inside the living cell, the toolbox is quite limited. In the case of enzyme-hydrolases for example, the choice is limited to organic molecules comprising a fluorescent dye (typically, 4-methylumbelliferone (MUmb) or 7-amino-4-methylcoumarin (AMC) derivatives) and a fluorescence quencher, bound via an enzyme-sensitive linker—so that when the linker is degraded, the fluorescent signal increases. Unfortunately, both MUmb and AMC are quenched and have a relatively low quantum yield in cells, and their excitation and emission ranges overlap with that of intracellular fluorophores, often producing a strong background noise. R6G, on the other hand, has excellent quantum yield apart from intracellular fluorophores, but there are no efficient quenchers that could be chemically linked to R6G. Herein, we show that R6G is able to form intermolecular FRET pairs with MUmb or AMC, with the latter serving as fluorescence donors. This yields a combination of R6G’s excellent fluorescence properties with a possibility to use an enzyme-sensitive linker in MUTMAC or AMC derivatives. This phenomenon was initially discovered in a model system, reversed micelles, where the donor, the acceptor, and the enzyme are forced to be in close proximity to each other, so that proximity could serve as an explanation for the intermolecular FRET effect. Surprisingly enough, the phenomenon has been reproduced in living cells. Moreover, we were able to create working intermolecular donor–acceptor FRET pairs for several different enzymes, including chymotrypsin, phosphatase, and asparaginase. This appears counterintuitive, as besides the overlap of the emission spectra of the donor and the absorption spectra of the acceptor, there are other criteria for the FRET effect, including the convergence of two fluorophores at a distance of about 1–10 nm, and the orientation of their dipoles at a certain angle, which is difficult to imagine in a bulk system like a living cell. We hypothesize that FRET-enabling donor–acceptor interaction may be taking place at the inner surface of the lipid bilayer, to which both donor and acceptor molecules would likely have an affinity. This hypothesis would require a more detailed investigation. Therefore, we have shown that the method suggested has good potential in the visualization of enzyme functioning inside living cells, which is often a challenging task. Shifting of the fluorescence signal to the long-wavelength region would increase the signal selectivity, making it easily distinguishable from autofluorescence. Full article

The production of public goods is a necessary condition for the survival of the species, but it comes at the expense of individual growth. In a prototype bacterial colony, we model the role of quorum sensing as a resource redistribution mechanism. Two types of bacterial colonies are analyzed, one made up of a single strain and one made up of two different strains. Based on a recent series of experimental data present in the literature, we analyze two types of strains with different extinction times: strains that consume available resources very quickly, therefore becoming extinct quickly, and strains that consume resources slowly and die due to aging. We show that the proposed quorum sensing model describes the main experimental result that coexistence may favor the survival of both strains. Furthermore, the production of public goods is maximized when both types of individuals have the maximum proliferation output. Finally, we highlight the role played by so-called dormant cells in the duration of survival time. These cells are of particular interest because their ability to counteract different types of stress (e.g., the use of antibiotics) still constitutes a challenge. Full article