DNA Flow-Stretch Assays for Studies of Protein-DNA Interactions at the Single-Molecule Level

Protein-DNA interactions are the core of the cell’s molecular machinery. For a long time, conventional biochemical methods served as a powerful investigatory basis of protein-DNA interactions and target search mechanisms. Currently single-molecule (SM) techniques have emerged as a complementary tool for studying these interactions and have revealed plenty of previously obscured mechanistic details. In comparison to the traditional ones, SM methods allow direct monitoring of individual biomolecules. Therefore, SM methods reveal reactions that are otherwise hidden by the ensemble averaging observed in conventional bulk-type methods. SM biophysical techniques employing various nanobiotechnology methods for immobilization of studied molecules grant the possibility to monitor individual reaction trajectories of biomolecules. Next-generation in vitro SM biophysics approaches enabling high-throughput studies are characterized by much greater complexity than the ones developed previously. Currently, several high-throughput DNA flow-stretch assays have been published and have shown many benefits for mechanistic target search studies of various DNA-binding proteins, such as CRISPR-Cas, Argonaute, various ATP-fueled helicases and translocases, and others. This review focuses on SM techniques employing surface-immobilized and relatively long DNA molecules for studying protein-DNA interaction mechanisms.

Spatial Sound in a 3D Virtual Environment: All Bark and No Bite?

Although the focus of Virtual Reality (VR) lies predominantly on the visual world, acoustic components enhance the functionality of a 3D environment. To study the interaction between visual and auditory modalities in a 3D environment, we investigated the effect of auditory cues on visual searches in 3D virtual environments with both visual and auditory noise. In an experiment, we asked participants to detect visual targets in a 360° video in conditions with and without environmental noise. Auditory cues indicating the target location were either absent or one of simple stereo or binaural audio, both of which assisted sound localization. To investigate the efficacy of these cues in distracting environments, we measured participant performance using a VR headset with an eye tracker. We found that the binaural cue outperformed both stereo and no auditory cues in terms of target detection irrespective of the environmental noise. We used two eye movement measures and two physiological measures to evaluate task dynamics and mental effort. We found that the absence of a cue increased target search duration and target search path, measured as time to fixation and gaze trajectory lengths, respectively. Our physiological measures of blink rate and pupil size showed no difference between the different stadium and cue conditions. Overall, our study provides evidence for the utility of binaural audio in a realistic, noisy and virtual environment for performing a target detection task, which is a crucial part of everyday behaviour—finding someone in a crowd.

Multi-Target Coordinated Search Algorithm for Swarm Robotics Considering Practical Constraints

In order to deal with the multi-target search problems for swarm robots in unknown complex environments, a multi-target coordinated search algorithm for swarm robots considering practical constraints is proposed in this paper. Firstly, according to the target detection situation of swarm robots, an ideal search algorithm framework combining the strategy of roaming search and coordinated search is established. Secondly, based on the framework of the multi-target search algorithm, a simplified virtual force model is combined, which effectively overcomes the real-time obstacle avoidance problem in the target search of swarm robots. Finally, in order to solve the distributed communication problem in the multi-target search of swarm robots, a distributed neighborhood communication mechanism based on a time-varying characteristic swarm with a restricted random line of sight is proposed, and which is combined with the multi-target search framework. For the swarm robot kinematics, obstacle avoidance, and communication constraints of swarm robots, the proposed multi-target search strategy is more stable, efficient, and practical than the previous methods. The effectiveness of this proposed method is verified by numerical simulations.