Biophysics and Physicobiology最新文献

Measuring physical quantities in the nanometric region inside single cells is of great importance for understanding cellular activity. Thus, the development of biocompatible, sensitive, and reliable nanobiosensors is essential for progress in biological research. Diamond nanoparticles containing nitrogen-vacancy centers (NVCs), referred to as fluorescent nanodiamonds (FNDs), have recently emerged as the sensors that show great promise for ultrasensitive nanosensing of physical quantities. FNDs emit stable fluorescence without photobleaching. Additionally, their distinctive magneto-optical properties enable an optical readout of the quantum states of the electron spin in NVC under ambient conditions. These properties enable the quantitative sensing of physical parameters (temperature, magnetic field, electric field, pH, etc.) in the vicinity of an FND; hence, FNDs are often described as "quantum sensors". In this review, recent advancements in biosensing applications of FNDs are summarized. First, the principles of orientation and temperature sensing using FND quantum sensors are explained. Next, we introduce surface coating techniques indispensable for controlling the physicochemical properties of FNDs. The achievements of practical biological sensing using surface-coated FNDs, including orientation, temperature, and thermal conductivity, are then highlighted. Finally, the advantages, challenges, and perspectives of the quantum sensing of FND are discussed. This review article is an extended version of the Japanese article, In Situ Measurement of Intracellular Thermal Conductivity Using Diamond Nanoparticle, published in SEIBUTSU BUTSURI Vol. 62, p. 122-124 (2022).

Single-molecule technologies can provide detailed information regarding molecular mechanisms and interactions that cannot easily be studied on the bulk scale; generally, individual molecular behaviors cannot be distinguished, and only average characteristics can be measured. Nevertheless, the development of the single-molecule sequencer had a significant impact on conventional in vitro single-molecule research, featuring automated equipment, high-throughput chips, and automated analysis systems. However, the utilization of sequencing technology in in vitro single-molecule research is not yet globally prevalent, owing to the large gap between highly organized single-molecule sequencing and manual-based in vitro single-molecule research. Here, we describe the principles of zero-mode waveguides (ZMWs) and nanopore methods used as single-molecule DNA sequencing techniques, and provide examples of functional biological measurements beyond DNA sequencing that contribute to a global understanding of the current applications of these sequencing technologies. Furthermore, through a comparison of these two technologies, we discuss future applications of DNA sequencing technologies in in vitro single-molecule research.

With the recent progress in structural biology and genome biology, structural dynamics of molecular systems that include nucleic acids has attracted attention in the context of gene regulation. The structure-function relationship is an important topic that highlights the importance of the physicochemical properties of nucleotides, as well as that of amino acids in proteins. Simulations are a useful tool for the detailed analysis of molecular dynamics that complement experiments in molecular biology; however, molecular simulation of nucleic acids is less well developed than that of proteins partly due to the physical nature of nucleic acids. In this review, we briefly describe the current status and future directions of the field as a guide to promote collaboration between experimentalists and computational biologists.

Ciliates are swimming microorganisms in aquatic environments. Habitats where ciliates accumulate include nutrient-rich solid-liquid interfaces such as pond bottom walls and waterweed surfaces. The ciliates stay near the walls to survive. We investigated the dynamics of the near-wall behavior of ciliates. In experiments, the ciliates were made to slide on a flat wall of glass substrate. When encountering the wall, the wall-side cilia of the cells stop their motion and lose their propelling activity, which indicates that the ciliates have a mechano-sensing system for cilia beating. Based on the experimental results, we hypothesized that the ciliary thrust force that propels the cell body becomes asymmetric, and the asymmetry of the thrust force generates a head-down torque to keep the cell sliding on the wall. To prove this hypothesis, we performed numerical simulations by using a developed hydrodynamic model for swimming ciliates. The model revealed that the loss of cilia activity on the wall side physically induces a sliding motion, and the aspect ratio of the cell body and effective cilium area are critical functions for the sliding behavior on a wall. In addition, we investigated the stability of the sliding motion against an external flow. We found that ciliates slide upstream on a wall. Interestingly, the dynamics of this upstream sliding, called rheotaxis, were also explained by the identical physical conditions for no-flow sliding. Only two simple physical conditions are required to explain the dynamics of ciliate survival behavior. This review article is an extended version of the Japanese article, Fluid Dynamic Model Reveals a Mechano-sensing System Underlying the Behavior of Ciliates, published in SEIBUTSU BUTSURI Vol. 61, p. 16-19 (2021).