Abstract: Evolution of SARS-CoV-2 has led to the emergence of variants with increased immune evasion capabilities, posing significant challenges to antibody-based therapeutics and vaccines. The cross-neutralization activity of antibodies against Omicron variants is governed by a complex and delicate interplay of multiple energetic factors and interaction contributions. In this study, we conducted a comprehensive analysis of the interactions between the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein and four neutralizing antibodies—S309, S304, CYFN1006, and VIR-7229. Using integrative computational modeling that combined all-atom molecular dy-namics (MD) simulations, mutational scanning, and MM-GBSA binding free energy calculations, we elucidated the structural, energetic, and dynamic determinants of antibody binding. Our findings reveal distinct dynamic binding mechanisms and evolutionary adaptation driving broad neutralization effect of these antibodies. We show that S309 targets conserved residues near the ACE2 interface, leveraging synergistic van der Waals and electrostatic interactions, while S304 focuses on fewer but sensitive residues, making it more susceptible to escape mutations. The analysis of CYFN-1006.1 and CYFN-1006.2 antibody binding highlights broad epitope coverage with critical anchors at T345, K440, and T346, enhancing its efficacy against variants carrying the K356T mutation which caused escape from S309 binding. Our analysis of broadly potent VIR-7229 antibody binding to XBB.1.5 and EG.5 Omicron variants emphasized a large and structurally complex epitope, demonstrating certain adaptability and compensatory effects to F456L and L455S mutations. Mutational profiling identified key residues crucial for antibody binding, including T345, P337, and R346 for S309, and T385 and K386 for S304, underscoring their roles as evolutionary "weak spots" that balance viral fitness and immune evasion. The results of this energetic analysis demonstrate a good agreement between the predicted binding hotspots and critical mutations with respect to the latest experiments on average antibody escape scores. The results of this study dissect distinct energetic mechanisms of binding and importance of targeting conserved residues and diverse epitopes to counteract viral resistance. Broad-spectrum antibodies CYFN1006 and VIR-7229, which maintain efficacy across multiple variants achieve neutralization by targeting convergent evolution hotspots while enabling tolerance to muta-tions in these positions through structural adaptability and compensatory interactions at the binding interface. The results of this study underscore the diversity of binding mechanisms employed by different antibodies and molecular basis for high affinity and excellent neutraliza-tion activity of the latest generation of antibodies.

Abstract: Blood samples and testing are routine in health care. Presently there is a growing interest in using tear samples in place of blood. Tear samples can be obtained non-invasively and collection does not require the skills of a trained phlebotomist. Red blood cells and other cells are not present in tears which avoids centrifugation. Importantly, basal tears samples contain most of the biomarkers present in blood. The difficulty is the small volume of basal tears which is about 7 μL in each eye. At present any contact with the eye results in additional reflex tears with a different chemical composition. The small tear samples are collected with capillary tubes and then sent out for amplified assays, such as enzyme-linked immunosorbent assay (ELISA) or polymerase chain reaction (PCR). The results are not available for days or a week and therefore less useful in an ophthalmology office. We propose the use of a contact lens which contains bound antibodies for fluorescence immunoassays. At present, the lenses could be removed from the patient for point-of-care measurements at the bedside. To prove this concept is possible we performed a three-protein layer capture assay which mimics an immunoassay. For convenience we used lysozyme (Lys) which spontaneously coats silicon hydrogel (SiHG) contact lenses (CL). Anti-lysozyme IgG was the second layer captured, anti-lysozyme was considered to be the target biomarker. The third layer was rhodamine or Alexa Fluor-labeled Ab against the IgG Fc region, considered to be the detection anti-body. The multiple protein layers were stable and did not wash off the SiHG lenses. These results strongly suggest the contact lens can be used for capture immunoassays for a wide variety of biomarkers.

Abstract: This paper proposes a novel hypothesis within the somatosensory domain: that the distribution of skin lines and pores contributes meaningfully to spatial and thermal sensory processing. While much attention has been given to tactile nerve endings and pressure receptors, the role of skin surface geometry remains underexplored. Based on anatomical observation and practical testing, we suggest that skin lines—especially in high-nerve-density areas—form dynamic micro-geometries that respond to physical contact by deforming in ways interpretable as tension, twist, or compression. In contrast, pore clusters may play a more pronounced role in slower thermosensory detection. This distinction introduces a structural layer to tactile identity resolution and supports the broader Faulkner Conical Method, in which perception arises through geometric collapse of environmental information.

Abstract: Platinum-based radiochemotherapy is associated with hematologic side effects, impacting patient outcomes. However, the mechanisms of action of cisplatin and its interaction with ionizing radiation (IR) are still not fully understood clinically and for biodosimetry in radiotherapy. For this purpose, healthy donors’ peripheral blood lymphocytes (PBLs) were pretreated with cisplatin in a pulse (1-4h) or continuous (24h) regime followed by X-rays. DNA damage was assessed as DNA double-strand breaks using repair foci of yH2AX and 53BP1 after 0.5h and 24h in G1 PBLs, and the proliferation-based cytokinesis-block micronucleus assay. Additionally, cell death and proliferation activity were measured. Unlike a 1h pulse, a 24h cisplatin pretreatment caused a concentration-dependent increase in cisplatin-induced foci while decreasing IR-induced foci, especially 24h after irradiation. This was accompanied by increased apoptosis, with cisplatin and IR having additive effects. Both genotoxins alone caused a dose-dependent increase in micronuclei, while cisplatin significantly reduced binuclear cells, especially after 24h treatment, leading to lower micronuclei frequencies post-irradiation. Our results show that prolonged cisplatin exposure, even at low concentrations, impacts the vitality and division activity of PBLs, with significantly stronger effects post-irradiation. This has major implications and must be considered for the detection of DNA damage-associated biomarkers in PBLs used in clinical prediction or biodosimetry during radiotherapy.

Abstract: Background: Hypertension and Chronic Kidney Disease (CKD) are interconnected conditions, with the activation of the transcription factor NF-κB playing a crucial role. Sildenafil used for erectile dysfunction and pulmonary hypertension, may exhibit anti-inflammatory effects by interacting and modulating the structure of NF-κB. Methods: We employed various computational techniques to explore the interaction between sildenafil and NF-κB, including molecular docking, molecular dynamics (MD) simulations, elastic network models, statistical potentials, and volumetric analyses of internal cavities. Results: Sildenafil induces conformational changes in NF-κB, potentially reducing its activity. Molecular docking showed sildenafil’s inhibitory potency is comparable to known anti-inflammatory compounds like resveratrol. MD simulations indicated that sildenafil destabilizes NF-κB’s structure, which may impact its biological function. Experimental validation was conducted using biopsies from hypertensive and kidney-damaged rat models, treated and untreated with sildenafil. Histological and immunoperoxidase analyses assessed cellular infiltration, kidney damage, and NF-κB expression, demonstrated that sildenafil treatment significantly reduced cellular infiltration, kidney damage, and NF-κB expression, confirming its anti-inflammatory properties. Conclusion: sildenafil’s potential to modulate NF-κB activity, offering a promising therapeutic strategy for managing hypertension and CKD. These preliminary findings suggest that sildenafil could be repurposed to provide comprehensive treatment for these conditions, leveraging its molecular and biochemical interactions with NF-κB.

Abstract: Blood analogs are widely employed in in-vitro experiments such as particle image velocity (PIV) to study hemodynamics, assisting pathophysiological diagnosis of neurovascular and cardiovascular diseases, as well as pre-surgical planning and intraoperative orientation. To obtain accurate physical parameters critical for diagnosis and treatment, blood analogs should exhibit realistic non-Newtonian shear-thinning features. In this study, two types of blood analogs were created to mimic the shear-thinning behavior of blood over a temperature range of 295 to 312 K. Type-I is a general-purpose analog composed of deionized (DI) water and Xanthan gum (XG) powder, while Type-II is specially designed for PIV tests, incorporating DI water, XG and fluorescent microspheres (450 ppm). By minimizing the root mean square deviation between the generated blood analog and an established viscosity model, formulas for both blood analogs were successfully derived for the designated temperature range. Results show both blood analogs can replicate the shear-thinning properties of real blood, with the averaged relative discrepancy < 5%. Additionally, a strong linear correlation was observed between body temperature and XG concentration in both blood analogs (coefficient of determination > 0.96): for Type-I, 295-312 K correlates with 140-520 ppm and for Type-II, 295-315 K correlates with 200-560 ppm. This work bridges the gap between idealized blood viscosity models and the complexities of real-world physiological conditions, offering a versatile platform for advancing hemodynamic research, optimizing therapeutic interventions, and enhancing biomedical technologies in temperature-sensitive environments.

Abstract: The homotrimeric P2X7 receptor (P2X7R) contains three ATP4- binding sites in its ectodomain. Here, we investigated the role of the individual ATP4- activation sites of the rat P2X7R (rP2X7R) using trimeric rP2X7R concatamers consisting either of three wild-type subunits (7-7-7) or concatamers with up to three subunits having knocked-out ATP binding sites (7ko-7ko-7ko). Following expression in Xenopus oocytes, ATP4--elicited ion currents were recorded using the two-microelectrode voltage clamp technique. The 7-7-7 concatamer exhibited a biphasic ATP4- concentration dependence, best fit by the sum of two Hill functions, confirming the existence of functionally distinct ATP4- activation sites. The activation time course of the 7-7-7 was best approximated by the sum of a fast and a slow exponential saturating activation component. Similarly, deactivation exhibited both a fast and a slow exponential decay. Only one Hill function was required to best fit the ATP4- concentration dependence of concatamers with only two or one ATP4- binding sites, and their deactivation time courses largely lacked the slowly deactivating components. We conclude that binding of one ATP4- is sufficient for partial activation of the rP2X7R and that allosteric effects occur when all three ATP4- binding sites are occupied, leading to distinct functional activation sites.

Abstract: System suitability testing of chromatography is an indispensable procedure in pharmaceutical analysis, and must comply with rules in related pharmacopoeias. An inverse Fourier transform algorithm is developed to accurately evaluate chromatographic features versus a standard Gaussian peak shape. The regular chromatogram is considered as a pseudo-frequency spectrum and can be converted to a nominal time signal by inverse Fourier transformation. The system suitability parameters of peak width, theoretical plate number, tailing factor and noise testing were evaluated by linear regressions directly and compared with the compendial rules. This novel method is simple, accurate, robust, reliable and efficient for evaluation of chromatographic peak features.

Abstract: A human brain can communicate with another brain using quantum entanglement. Similar particles can become entangled without direct interaction. Sensory communication between two individuals over long distances is not yet fully understood. In this research, the transfer of information based on entanglement between the brains of two people was investigated. The test was conducted on two individuals located far apart. These individuals were exposed to similar music and, based on their neural plasticity, both were placed in the same state. By activating the brain's reward system, coherent thinking was induced in the brains of these individuals. Then, through entanglement, compressed information was transmitted and received between them. Decoding compressed information is the key to transmitting information based on entanglement between identical particles.

Abstract: Although evolutionary theory has yet to fully explain why natural selection occurs, it is crucial to recognize that this phenomenon extends beyond biological systems and is evident in physical systems as well. Specifically, in compliance with the second law of thermodynamics, isolated and closed non-equilibrium systems tend to progress toward states in which entropy increases. When there are multiple pathways for entropy production, such systems will select combinations of pathways that maximize the rate of entropy production from among the available paths. This is known as the fourth law of thermodynamics. Life processes represent one way to achieve increased entropy in nature. Genetic mutations produce organisms with differing rates of entropy production, and when these organisms coexist, they form combinations of pathways with varying rates of entropy production. Nature selects among these possible combinations, selecting those that achieve the fastest rates of entropy production, thereby driving the evolution of life. The process of life’s evolution essentially involves exploring and selecting pathways that achieve fast entropy production across different free energy reservoirs through random mutation. As genetic mutations continue and nature persistently selects for faster entropy production rate, information accumulates, further accelerating the rate of entropy production. This physical selection for the pathways that minimize potential or maximize entropy at the fastest possible rate given the constraints, serves as a fundamental driver of the origin and evolution of life.

Abstract:

Low-frequency electromagnetic fields, induced by alternating current, are known to influence physicochemical properties and functioning of enzymes, including their catalytic activity. Herein, by using atomic force microscopy (AFM) and spectrophotometry analysis in parallel, we have investigated how the incubation near an autotransformer operated at 50 Hz influences the physicochemical properties of horseradish peroxidase (HRP). We have found that 30 min incubation of the enzyme above the coil of a loaded autotransformer enhances a disaggregation of HRP on mica and the number of adsorbed enzyme particles by two orders of magnitude in comparison with the control sample. And most interestingly, the incubation of HRP above the switched-off transformer for the same period of time has been found to cause a disaggregation of the enzyme, An increase in the activity of HRP against ABTS has been observed in the both cases. We hope that the interesting effects reported will emphasize the importance of consideration of the influence of low-frequency electromagnetic fields on enzymes in the design of laboratory and industrial equipment intended for operation with enzyme systems.

Abstract:

The dynamic phosphorylation of the human RNA Pol II CTD establishes a code applicable to all eukaryotic transcription processes. However, the ability of these specific post-translational modifications to convey molecular signals through structural changes remains unclear. We previously explained that each gene can be modeled as a combination of n circuits connected in parallel. RNA Pol II accesses these circuits and, through a series of pulses, matches the resonance frequency of the DNA qubits, enabling it to extract genetic information and quantum teleport it. Negatively charged phosphates react under RNA Pol II catalysis, increasing the electron density on the deoxyribose acceptor carbon. The first pulse of phosphorylation connects tyrosine to the nitrogenous base, while the subsequent pulses link the protein to molecular water through hydrogen bonds. The coupling of hydrogen proton transfer with electron transfer in water generates a supercurrent, which is explained by the correlation of pairs of the same type of fermions exchanging a boson. All these changes lead to the formation of a molecular protein-DNA-water condensate.

Abstract: The light reactions of oxygenic photosynthesis are performed by protein complexes embedded in the lipid bilayer of thylakoid membranes (TMs). Bilayers provide optimal conditions for the build-up of the proton motive force (pmf) and ATP synthesis. However, functional plant TMs, besides the bilayer, contain an inverted hexagonal (HII) phase and isotropic phases; a lipid polymorphism due to their major, non-bilayer lipid species, monogalactosyldiacylglycerol (MGDG). The lipid phase behavior of TMs is explained within the framework of the Dynamic Exchange Model (DEM), an extension of the fluid-mosaic model. DEM portrays the bilayer phase as inclusions between photosynthetic supercomplexes – characterized by compromised membrane impermeability and restricted sizes inflicted by the segregation propensity of lipid molecules, safe-guarding the high protein density of TMs. Isotropic phases mediate membrane fusions and are associated with the lumenal lipocalin-like enzyme, violaxanthin de-epoxidase. Stromal-side proteins surrounded by lipids give rise to HII phase. These features instigate experimentally testable hypotheses: (i) non-bilayer phases mediate functional sub-compartmentalization of plant chloroplasts – a quasi-autonomous energization and ATP synthesis of each granum-stroma TM assembly; and (ii) the generation and utilization of pmf depend on hydrated protein networks and proton-conducting pathways along membrane surfaces – rather than on strict impermeability of the bilayer.

Abstract: Using the normal dynamic anatomy of the left heart and aorta as an example, it has been shown that the streamlined surfaces of the flow channels in this segment of the circulation can be approximated with sufficient accuracy by the dependences for the streamlines resulting from the exact solution of the basic equations of hydrodynamics for the class of centripetal swirling viscous fluid flows. It has been shown that in three consecutive segments of the blood channel from the left atrium to the end of the aorta, at the moment of maximum flow velocity, the geometrical configuration of the channel satisfies the condition of constancy of the product of the longitudinal and the square of the radial coordinate, and the zone of jet initiation is limited by a concave streamlined surface. The curvature of the flow channel axis has no effect on the hydrodynamic structure of the flow, since it is coherent with the directions of the streamlines.

Abstract: Cold-active enzymes hold promise in energy-efficient processes. Amylases are widely used in household and industrial applications, but only a few are cold-active. Here we describe three novel secreted amylases Rho13, Ika2 and I3C6, all from bacteria growing in the cold and alkaline ikaite columns in Greenland. They all hydrolysed starch to smaller malto-oligomers, but only Rho13 and Ika2 hydrolysed cyclodextrins and only Ika2 displayed transglycosylation activity. Ika2 forms a stable dimer, while both Rho13 and I3C6 are mainly monomeric. They all have optimal temperatures around 30-35℃ and significant activity below 20℃, but Rho13 and I3C6 had an alkaline pH optimum while Ika2 was markedly acidophilic. They show complex dependence on Ca2+ concentration, with activity of Rho13 and I3C6 following a bell-shaped dependence and Ika2 being unaffected; however, removal of Ca2+ reduces stability of all 3 enzymes. Loss of structure occurs well above the optimal activity, showing the characteristic psychrophilic divorce be-tween activity and stability. MD simulations showed that Ika2 did not have a well-defined Ca2+ binding site, while Rho13 and I3C6 both maintain one stably bound Ca2+ ion. We identified psychrophilic features as higher levels of backbone fluctuations compared to mesophilic counterparts, founded in a lower number of internal hydrogen bonds and salt bridges. This increased fluctuation is also found in regions outside the active site and may provide easier substrate access and ac-commodation and faster barrier transitions. Our work sheds further light on the many ways in which psychrophilic enzymes adapt to increased catalysis at lower temperatures.

Abstract:

von Willebrand factor (vWF) is a large glycoprotein in circulation system, which senses hydrodynamic force at vascular injuries and then recruits platelets in assembling clots. How vWF mechanosenses shear flow for molecular unfolding is an important topic. Here, Förster resonance energy transfer (FRET) biosensor was developed to monitor vWF conformation change to hydrodynamic force. The full-length vWF-based biosensor is anchored on cell surface, in which A2 domain is flanked with FRET pair. With 293T cells seeded into microfluidic channels, 2.8 dyn/cm2 shear force induced remarkable FRET change (~60%) in 30 min. Gradient micro-shear below 2.8 dyn/cm2 demonstrated FRET responses positively related to flow magnitudes with 0.14 dyn/cm2 inducing obvious change (~16%). The FRET increases indicate closer positioning of A2’s two termini in vWF, supported with high FRET of A2 only-based biosensor, which probably resulted from flow-induced A2 dissociation from vWF intramolecular binding. Interestingly, gradual increase of flow from 2.8 to 28 dyn/cm2 led to decreasing FRET changes, suggesting the second-level unfolding in A2 domain. LOCK-vWF biosensor with bridged A2 two termini or A2 only biosensor couldn’t sense the shear, indicating structure-flexible A2 and large vWF molecules important in the mechanosensation. In conclusion, the developed vWF-based biosensor demonstrated high mechanosensation of vWF with two-level unfolding to shear force: the dissociation of A2 domain from vWF intramolecular binding under micro shear, and then unfolding of A2 in vWF under higher shear. This study provides new insights on vWF mechanosensitive feature for its physiological functions and implicated disorders.

Abstract: Bacteriorhodopsin (BR) is a photosensitive membrane protein commonly found in Archaea, bacteria, and eukaryotes. Its biological function involves transferring protons from the cytoplasmic side to the extracellular side, converting light energy into chemical energy through ATP synthesis. Because of its simple structure and stable function, it has been widely studied in the field of optogenetics. The Halorubrum sp. Ejinoor Archaerhodopsin （HeAR）was discovered in a salt lake in Inner Mongolia, China, and shares 57% homology with BR. In this study, HeAR was expressed in E. Coli BL21(DE). Biological function of HeAR was analyzed by SDS-PAGE, UV-VIS absorption spectrum, CD spectrum, laser flash photolysis and proton pump activity detection. The results indicated that HeAR was purple and demonstrated light-dark adaptation. The maximum absorbance wavelengths for dark-adapted HeARD and light-adapted HeARL were 550 nm and 560 nm, respectively. The ratio of All-trans and 13-cis chromophore was 2:1 in HeARD and 6:1 in HeARL. The CD spectrum showed that HeAR also has trimer structure. HeAR was also a proton pump and the photochemical reaction cycle was 100 ms. Although there were L, M, N and O intermediates similar to BR in HeAR. However, the generation and disappearance time of M state is earlier than that of BR and the M state disappears before the O state. It is likely that other intermediates exist, resulting in a slow cycle. HeAR, as a photosensitive tool, may have promising applications in the field of optogenetics.

Abstract: Objective: The air content within the lungs directly influences the dielectric properties of lung tissue; however, existing studies have been conducted under ex vivo conditions and without quantitatively controlling air volume. The study aims to develop an improved model using in vivo measurements to accurately characterize the dielectric properties of rabbit lung tissue across various tidal volumes, based on the Kramers-Kronig (KK) relationships. Methods: In this study, six sets of different tidal volumes (30, 40, 50, 60, 70, 80 mL) were set in the frequency band of 100 MHz~1 GHz to analyze the trend of the dielectric properties, and the dielectric parameters were systematically constructed under the conditions of different tidal volumes. Results: It was found that the conductivity and permittivity of rabbit lung tissue showed a decreasing trend with increasing tidal volume in the measuring frequency band. The traditional Cole-Cole model has limitations in simulating the dielectric properties of in vivo lung tissues. Therefore, by refining and optimizing the model based on the KK relationships, while ensuring physical plausibility, the study successfully reduced the average error between the measured data and the model predictions to less than 5%. Conclusions: It lays the groundwork for investigating the relationship between total air volume within the lungs and their dielectric properties in vivo.

Abstract: Bioelectric membrane potentials regulate cellular growth, differentiation, and movement. Disruptions in bioelectric signaling are strongly linked to cancer development, particularly in breast cancer, where ion channel dysfunction and neuroreceptor-related pathways play significant roles in the cell cycle, epithelial-mesenchymal transition, angiogenesis, inflammation, the tumor microenvironment, and tumor progression. Neuroreceptors are critical not only in initiating and advancing cancer but also in conferring resistance to treatments. Advances in understanding these biological mechanisms could lead to more cost-effective and less invasive therapeutic strategies to treat tumors. This review explores the expanding evidence connecting bioelectric activity to breast cancer, focusing on neuroreceptor pharmacology as a transformative therapeutic approach. Investigating how neuroreceptor pharmacology-based modulation of bioelectricity affects breast cancer progression and integrating these insights into therapeutic development offers a promising path for addressing treatment challenges and improving precision in managing aggressive cancer subtypes.

Abstract: Myo-inositol-1,2,3,4,5,6-hexakisphosphate (IP6), commonly found in plant-derived foods, has important pharmacological properties against many pathological processes. One of them could be the neurodegeneration, stimulated by a dysregulated metal metabolism. Consequently, we explore here the role of IP6 in mitigating neurodegenerative processes catalyzed by dysregulated free iron. Using dopamine and ascorbic acid as models of neuronal redox systems, we demonstrate that IP6 effectively chelates Fe³⁺, inhibiting its ability to catalyse the oxidative degradation of DA and AA. Our findings reveal that IP6 prevents the formation of harmful intermediates such as neuromelanin and reactive oxygen species, which are associated with neuronal damage. Furthermore, we examined the effect of IP6 on Fe³⁺-induced protein aggregation, focusing on α-synuclein, a protein directly linked to Parkinson's disease. IP6 altered the aggregation mechanism of αS by accelerating the conversion of toxic oligomers into less harmful amyloid fibrils, thus reducing the potential for neuronal damage. Our results highlight the dual function of IP6 as potent Fe³⁺ chelator and modulator of protein aggregation pathways, thus emphasizing its potential as a neuroprotective agent. Consequently, IP6 offers promising therapeutic features for mitigating the progression of neurodegenerative disorders such as Parkinson’s and Alzheimer’s diseases.