Biophysics and physicobiology最新文献

Cyanobacteria can produce alkanes equivalent to diesel fuels through a two-step enzymatic process involving acyl-(acyl carrier protein) reductase (AAR) and aldehyde deformylating oxygenase (ADO), providing a potential renewable biofuel source. AAR binds to ADO for efficient delivery of an aldehyde substrate and they have been proposed to dissociate when the alkane product is released from the same site as the substrate entrance of ADO. However, the dynamics of the substrate and product in ADO during substrate entry and product release are poorly understood. Here, we performed molecular dynamics (MD) simulations of ADO in the presence of substrate or product. We found that while the aldehyde substrate remains close to the active center of ADO before catalysis, the alkane product can dynamically rotate within the hydrophobic tunnel inside ADO toward the product exit after catalysis. Furthermore, the parallel cascade selection (PaCS)-MD simulations of ADO and the AAR/ADO complex identified the locations of the substrate entrance and the multiple exits for product release on ADO. Strikingly, the PaCS-MD simulations revealed that the alkane product can be released from the exit different from the substrate entrance without dissociation of AAR. Based on these results, we propose a reaction model for efficient alkane production by the AAR/ADO complex in which aldehydes and alkanes are synthesized simultaneously while AAR and ADO remain bound, and the aldehyde substrate can be delivered to ADO immediately after alkane release. Our study will be useful in improving the efficiency of bioalkane production using AAR and ADO.

Transport networks spanning the entire body of an organism are key infrastructures for achieving a functional system and facilitating the distribution of nutrients and signals. The large amoeba-like organism Physarum polycephalum has gained attention as a useful model for studying biological transport networks owing to its visible and rapidly adapting vein structure. Using particle-tracking velocimetry, we measured the flow velocity of protoplasmic streaming over the entire body of Physarum plasmodia during the development of its intricate vein network. Based on these measurements, we estimated how the protoplasm is transported and mixed throughout the body. Our findings suggest that the vein network significantly enhances effective mixing of the protoplasm throughout the organism, which may have important physiological implications for nutrient distribution and signaling.

Chronic pain is an unpleasant experience caused by sensory and emotional instability, sometimes independent of actual tissue damage. Pain relief can greatly impact psychologic, social, and economic well-being. Aromatherapy has long been used to alleviate pain and previous studies demonstrated that odors alter cerebral blood flow. In the present study, we used near-infrared spectroscopy to test our hypothesis that olfactory stimulation contributes to pain relief by altering cerebral blood flow in brain regions associated with pain. Pain was induced by transcutaneous electrical stimulation and assessed using a visual analog scale. Peppermint and lavender olfactory stimuli were used. Based on previous results, we focused on the prefrontal cortex. A placebo experiment in which only air stimulation was presented revealed minimal changes in blood flow in the ventromedial prefrontal cortex when comparing pain stimulation alone and a combination of placebo and pain stimulation. We then examined changes in blood flow following the presentation of peppermint or lavender scents. Significant differences in blood flow were observed in the dorsolateral prefrontal cortex (DLPFC) between pain stimulation alone and pain stimulation combined with odor stimulation. These findings supported our previous finding that the DLPFC is involved in pain relief by patch-adhered stimulation, but odor stimulation activated the right DLPFC whereas patch-adhered stimulation suppressed the left DLPFC. One interpretation of the discrepancy is that the contrast of activation between the right and left DLPFC is important in pain relief. Our research will help to elucidate the neurologic mechanisms underlying pain relief.

Neurons have an ionic system with several types of ion pumps and ion channels on their membranes. Each ion pump creates a specific difference in ion concentration inside and outside the neuron, and the energy resulting from this difference in concentration is maintained inside the neuron as a resting potential. Each ion channel senses the necessary situation, opens the channel, and allows the corresponding ion to pass through to perform its corresponding role. This ionic system realizes important functions such as (i) fast conduction of action potentials, (ii) achieving synaptic integration in response to several inputs with a time lag, and (iii) the information processing functions by neural circuits. However, the mechanisms by which these functions are realized have remained unclear. Therefore, based on the reports on various highly polymeric ion pumps, ion channels, cell membranes, and other components that have been elucidated so far, author analyzed how this ionic system can realize the above important functions from an electrical circuit designer point of view. As a result of a series of analyses, it was found that neurons realize each function by making full use of high-density packaging technology based on basic electrical principles and making maximum use of the extremely high dielectric properties of the ionic fluid of neurons. In other words, neuron looks to equip well designed ionic system which is the collaboration by designers of proteins and membranes that perform advanced functions and designers of electrical circuits that utilize them to achieve important functions electrically.

Four medicinal plants C. quadrangulare, D. linearis, P. adenophylla, and G. schomburgkiana growing in the South of Vietnam were investigated for their alpha-glucosidase inhibition. The crude methanol extract of C. quadrangulare was determined to be the most active extract, then was selected for further in vivo assays including antidiabetic study and toxicity. In vitro alpha-glucosidase inhibition of four medicinal plants C. quadrangulare, D. linearis, P. adenophylla, and G. schomburgkiana was screened using standard procedures. In vivo antidiabetic activity, acute toxicity and subchronical toxicity of C. quadrangulare leaves was assessed on Swiss albino mice. Swiss albino mice were induced with diabetes by intraperitoneal injection of alloxan at a dose of 150 mg/kg body weight. High-performance liquid chromatography with evaporative light scattering detector (HPLC-ELSD) were used to detect the bioactive components of C. quadrangulare leaves. All crude extracts from the studied plants showed promising alpha-glucosidase inhibition, with IC₅₀ values ranging from 2.4 to 35.3 μg/mL. The methanol extract of C. quadrangulare leaves was determined to be the most active extract. This extract was then selected for antidiabetic assay using alloxan induced model of type 2 diabetes mellitus mice. The results indicated that the extract at a dose of 400 mg/kg can effectively decrease blood glucose levels that is comparable to that of glibenclamide 2 mg/kg. This compound showed moderate activity toward alpha-glucosidase. Therefore, our study indicated that C. quadrangulare, D. linearis, P. adenophylla, and G. schomburgkiana extract are potential materials for producing α-glucosidase inhibitor drugs.

This is a report on the participation in the IUPAB Congress held in Kyoto in 1978 and 2024 by two senior members of the Biophysical Society of Japan who had the fortunate opportunity to attend the two Congresses. The authors comprehensively compared research presentations (poster presentations and oral presentations) at the two Congresses, which were half a century apart, and considered the academic changes in biophysics. It has been reported that biophysics has changed significantly over the past half century in line with technological advances of the times, and the next stage of biophysics is foreseen as an extension of the trend.

The action potential of cardiomyocytes is controlled by electrolytes in serum such as Na⁺, K⁺ and Ca²⁺. Hyperkalemia, which refers to an abnormally high concentration of K⁺ in the blood, can induce lethal arrythmia. In this study, the extracellular potentials on a sheet of chick embryonic cardiomyocytes were investigated at increasing K⁺ concentrations using a multielectrode array system. We observed that the interspike interval (ISI) was prolonged by approximately 3.5 times; dV/dt (the slope of a waveform) was decreased by more than five times; the field potential duration (FPD) was shortened by 20%, and the conduction velocity was about half at 12 mM K⁺ against the control (4 mM K⁺). In calcium therapy for hyperkalemia, although the prolongation of ISI under hyperkalemic conditions was restored, the slowing of conduction velocity, the decrease in dV/dt, and the shortening of FPD were not recovered by increasing the extracellular Ca²⁺ concentration. These findings provide a comprehensive understanding of cardiomyocytes in hyperkalemic conditions. Electrophysiological analysis by varying the extracellular concentrations of multiple types of electrolytes will be useful for the further discussion of the results of this study and for the interpretation of the waveforms obtained by measuring the extracellular potential.

JCVI-syn3B (syn3B), a minimal synthetic bacterium that only possesses essential genes, facilitates the examination of heterogeneous gene functions in minimal life. Conventionally, Escherichia coli is used to construct DNA fragments for gene transfer into the syn3B genome through Cre/loxP system. However, the construction process is challenging and time-consuming due to various issues, including the inhibition of E. coli growth and unexpected recombination, especially with AT-rich DNA sequences such as those found in Mycoplasma genes. Therefore, in this study, we aimed to develop a new transformation method to overcome these issues. We assembled the vector and target DNA fragments using an in vitro homologous recombination system and subsequently transferred the products into the syn3B genome. We obtained approximately 10³~10⁴ recombinant colonies per milliliter of the original culture in eight days, which is four days shorter than the conventional period, without any recombination issues, even for AT-rich DNA. This method may be applicable to other gene manipulation systems based on Cre/loxP system.