Peppy: A virtual reality environment for exploring the principles of polypeptide structure

A key learning outcome for undergraduate biochemistry classes is a thorough understanding of the principles of protein structure. Traditional approaches to teaching this material, which include two‐dimensional (2D) images on paper, physical molecular modeling kits, and projections of 3D structures into 2D, are unable to fully capture the dynamic 3D nature of proteins. We have built a virtual reality application, Peppy, aimed at facilitating teaching of the principles of protein secondary structure. Rather than attempt to model molecules with the same fidelity to the underlying physical chemistry as existing, research‐oriented molecular modelling approaches, we took the more straightforward approach of harnessing the Unity video game physics engine. Indeed, the simplicity and limitations of our model are strengths in a teaching context, provoking questions and thus deeper understanding. Peppy allows exploration of the relative effects of hydrogen bonding (and electrostatic interactions more generally), backbone φ/ψ angles, basic chemical structure, and steric effects on a polypeptide structure in an accessible format that is novel, dynamic, and fun to use. Apart from describing the implementation and use of Peppy, we discuss the outcomes of deploying Peppy in undergraduate biochemistry courses.     

Conditional strategies and interpopulation variation in the behaviour of jumping spiders

Abstract

Conditional strategies and interpopulation variation in the mating and predatory behaviour of salticid spiders are reviewed. A functional approach is adopted, and defended, in which specified behavioural phenotypes are accounted for, in large part, by specified selection factors. Courtship versatility, in which a male's behaviour depends on the female's maturity and location, is common in the Salticidae. If a male encounters an adult female in the open, where there is ample ambient light, he performs vision-dependent displays (Type 1 courtship) in front of her. If he encounters an adult female inside her nest, he uses different displays (Type 2 courtship) which are not vision–dependent and consist of various tugging, probing and jerking movements on the silk of the nest. These displays apparently send vibratory stimuli to the female. When a male encounters a subadult female inside her nest, he initially performs Type 2 courtship, then spins a second chamber on the nest and cohabits until the female moults and matures. A modification of optimal foraging theory has been used to examine factors that influence interpopulation variation in male courtship persistence. A study of five populations corroborated predictions from the model. Persistence appears to be related to female availability. Female availability is related to local phenology, which is, in turn, related to local climate. Complex examples of predatory versatility also have evolved in the Salticidae, especially in the genus Portia. All species of Portia studied are araneophagic spiders that invade other spiders' webs and practise aggressive mimicry. Portia fimbriata, uniquely among Portia species studied, uses specialised behaviour to prey on other salticids. Portia fimbriata and one of the salticids on which it preys, Euryattus sp., appear to be co-adapted to each other.     

Visualizing biomolecular electrostatics in virtual reality with UnityMol‐APBS

Virtual reality is a powerful tool with the ability to immerse a user within a completely external environment. This immersion is particularly useful when visualizing and analyzing interactions between small organic molecules, molecular inorganic complexes, and biomolecular systems such as redox proteins and enzymes. A common tool used in the biomedical community to analyze such interactions is the Adaptive Poisson‐Boltzmann Solver (APBS) software, which was developed to solve the equations of continuum electrostatics for large biomolecular assemblages. Numerous applications exist for using APBS in the biomedical community including analysis of protein ligand interactions and APBS has enjoyed widespread adoption throughout the biomedical community. Currently, typical use of the full APBS toolset is completed via the command line followed by visualization using a variety of two‐dimensional external molecular visualization software. This process has inherent limitations: visualization of three‐dimensional objects using a two‐dimensional interface masks important information within the depth component. Herein, we have developed a single application, UnityMol‐APBS, that provides a dual experience where users can utilize the full range of the APBS toolset, without the use of a command line interface, by use of a simple graphical user interface (GUI) for either a standard desktop or immersive virtual reality experience.     

Place illusion and plausibility can lead to realistic behaviour in immersive virtual environments

In this paper, I address the question as to why participants tend to respond realistically to situations and events portrayed within an immersive virtual reality system. The idea is put forward, based on the experience of a large number of experimental studies, that there are two orthogonal components that contribute to this realistic response. The first is ‘being there’, often called ‘presence’, the qualia of having a sensation of being in a real place. We call this place illusion (PI). Second, plausibility illusion (Psi) refers to the illusion that the scenario being depicted is actually occurring. In the case of both PI and Psi the participant knows for sure that they are not ‘there’ and that the events are not occurring. PI is constrained by the sensorimotor contingencies afforded by the virtual reality system. Psi is determined by the extent to which the system can produce events that directly relate to the participant, the overall credibility of the scenario being depicted in comparison with expectations. We argue that when both PI and Psi occur, participants will respond realistically to the virtual reality.     

Effects of Kinect-based virtual reality game training on upper extremity motor recovery in chronic stroke

Background: Therapeutic benefits of Kinect-based virtual reality (VR) game training in rehabilitation encourage its use to improve motor function.

Objective: To assess the effects of Kinect-based VR training on motor recovery of the upper extremity and functional outcomes in patients with chronic stroke.

Methods: In this randomized controlled trial, group A received 20 sessions of physical therapy (PT)?+?20 sessions of Kinect-based VR training and group B received only 20 sessions of PT. Clinical outcome measures were assessed at baseline and at the end of the treatments. Primary outcome measures that assess stroke patients’ motor function included upper extremity (UE) Fugl-Meyer Assessment (FMA). Secondary outcome measures were Brunnstrom Recovery Stages (BRS), Modified Ashworth Scale (MAS), Box and Block test (BBT), Motricity index (MI), and active range of motion (AROM) measurement.

Results: Statistically significant improvements in game scores (p?p?Conclusions: To conclude, our results suggest that the adjunct use of Kinect-based VR training may contribute to the improvement of UE motor function and AROM in chronic stroke patients. Further studies with a larger number of subjects with longer follow-up periods are needed to establish its effectiveness in neurorehabilitation.     

An integrated haptic-enabled virtual reality system for orthognathic surgery planning

Conventional Orthognathic surgery (OGS) planning involves cephalometric analyses and dental casts to be mounted on an articulator. Dental segments are subsequently identified, cut and repositioned to allow the fabrication of intraoral wafers that guide the positioning of the osteotomy bone segments. This conventional planning introduces many inaccuracies that affect the post-surgery outcomes. Although computer technologies have advanced computational tools for OGS planning, they have failed in providing a practical solution. Many focuses only on some specific stages of the planning process, and their ability to transfer preoperative planning data to the operating room is limited. This paper proposes a new integrated haptic-enabled virtual reality (VR) system for OGS planning. The system incorporates CAD tools and haptics to facilitate a complete planning process and is able to automatically generate preoperative plans. A clinical pre-diagnosis is also provided automatically by the system based on the patient’s digital data. A functional evaluation based on a real patient case study demonstrates that the proposed virtual OGS planning method is feasible and more effective than the traditional approach at increasing the intuitiveness and reducing errors and planning times.     

Maternal care and subsocial behaviour in spiders

While most spiders are solitary and opportunistically cannibalistic, a variety of social organisations has evolved in a minority of spider species. One form of social organisation is subsociality, in which siblings remain together with their parent for some period of time but disperse prior to independent reproduction. We review the literature on subsocial and maternal behaviour in spiders to highlight areas in which subsocial spiders have informed our understanding of social evolution and to identify promising areas of future research. We show that subsocial behaviour has evolved independently at least 18 times in spiders, across a wide phylogenetic distribution. Subsocial behaviour is diverse in terms of the form of care provided by the mother, the duration of care and sibling association, the degree of interaction and cooperation among siblings, and the use of vibratory and chemical communication. Subsocial spiders are useful model organisms to study various topics in ecology, such as kin recognition and the evolution of cheating and its impact on societies. Further, why social behaviour evolved in some lineages and not others is currently a topic of debate in behavioural ecology, and we argue that spiders offer an opportunity to untangle the ecological causes of parental care, which forms the basis of many other animal societies.     

Convergent evolution of eye ultrastructure and divergent evolution of vision-mediated predatory behaviour in jumping spiders

All jumping spiders have unique, complex eyes with exceptional spatial acuity and some of the most elaborate vision-guided predatory strategies ever documented for any animal of their size. However, it is only recently that phylogenetic techniques have been used to reconstruct the relationships and key evolutionary events within the Salticidae. Here, we used data for 35 species and six genes (4.8 kb) for reconstructing the phylogenetic relationships between Spartaeinae, Lyssomaninae and Salticoida. We document a remarkable case of morphological convergence of eye ultrastructure in two clades with divergent predatory behaviour. We, furthermore, find evidence for a stepwise, gradual evolution of a complex predatory strategy. Divergent predatory behaviour ranges from cursorial hunting to building prey-catching webs and araneophagy with web invasion and aggressive mimicry. Web invasion and aggressive mimicry evolved once from an ancestral spartaeine that was already araneophagic and had no difficulty entering webs due to glue immunity. Web invasion and aggressive mimicry was lost once, in Paracyrba, which has replaced one highly specialized predation strategy with another (hunting mosquitoes). In contrast to the evolution of divergent behaviour, eyes with similarly high spatial acuity and ultrastructural design evolved convergently in the Salticoida and in Portia.     

Secondary eyes mediate the response to looming objects in jumping spiders (Phidippus audax,Salticidae)

Some species have sensory systems divided into subsystems with morphologically different sense organs that acquire different types of information within the same modality. Jumping spiders (family Salticidae) have eight eyes. Four eyes are directed anteriorly to view objects in front of the spider: a pair of principal eyes track targets with their movable retinae, while the immobile anterior lateral (AL) eyes have a larger field of view and lower resolution. To test whether the principal eyes, the AL eyes, or both together mediate the response to looming stimuli, we presented spiders with a video of a solid black circle that rapidly expanded (loomed) or contracted (receded). Control spiders and spiders with their principal eyes masked were significantly more likely to back away from the looming stimulus than were spiders with their AL eyes masked. Almost no individuals backed away from the receding stimulus. Our results show that the AL eyes alone mediate the loom response to objects anterior to the spider.     

The evolution of eyes and visually guided behaviour

The morphology and molecular mechanisms of animal photoreceptor cells and eyes reveal a complex pattern of duplications and co-option of genetic modules, leading to a number of different light-sensitive systems that share many components, in which clear-cut homologies are rare. On the basis of molecular and morphological findings, I discuss the functional requirements for vision and how these have constrained the evolution of eyes. The fact that natural selection on eyes acts through the consequences of visually guided behaviour leads to a concept of task-punctuated evolution, where sensory systems evolve by a sequential acquisition of sensory tasks. I identify four key innovations that, one after the other, paved the way for the evolution of efficient eyes. These innovations are (i) efficient photopigments, (ii) directionality through screening pigment, (iii) photoreceptor membrane folding, and (iv) focusing optics. A corresponding evolutionary sequence is suggested, starting at non-directional monitoring of ambient luminance and leading to comparisons of luminances within a scene, first by a scanning mode and later by parallel spatial channels in imaging eyes.     

Snapper rest where they see best: visually mediated choice behaviour of Australasian snapper (Chrysophrys auratus)

The sensory physiology and behaviour of many fish species are strongly affected by light. This short study demonstrates that in the Australasian snapper (Chrysophrys auratus) absolute light intensity governs visual acuity and also guides preference behaviour, with fish choosing to ‘rest where they see best’. Use of the optomotor response to test visual acuity at four light intensities (0.01, 0.05, 1 and 3 μmol s^?1 m²), showed that visual acuity (measured as directional bias) was best at a light intensity of 0.05 μmol s^?1 m² (84.9% directional bias), but weakened at the highest and lowest light intensity (41.1 and 35.3%). When provided with a choice of the same four light environments fish also spent most time in the 0.05 μmol s^?1 m² light environment, while the highest and lowest intensity light environments were usually avoided. Acclimated light intensity (that is daytime light intensity of the home aquarium) was also 0.05 μmol s^?1 m²_. By selecting an environment where visual function is optimised, C. auratus are also optimising the ability to search for prey and to detect predators. The results are discussed with reference to habitat utilisation and thoughts for trawl fishing practices.     

A quantitative method for evaluation of 6 degree of freedom virtual reality systems

Modern virtual reality systems such as the HTC Vive enable users to be immersed in a virtual world. Validation of the HTC Vive and other contemporaneous systems for use in clinic, research, and industry applications will assure users and developers that games and applications made for these systems are accurate representations of the real world. The purpose of this study was to develop a standardized method for testing the translational and rotational capabilities of VR systems such as the HTC Vive. The translational and rotational capabilities of the HTC Vive were investigated using an industry grade robot arm and a gold standard motion capture system. It was found that the average difference between reported translational distances traveled was 0.74 ± 0.42 mm for all room-scale calibration trials and 0.63 ± 0.27 mm for all standing calibration trials. The mean difference in angle rotated was 0.46 ± 0.46° for all room-scale calibration trials and 0.66 ± 0.40° for all standing calibration trials. When tested using human movement, the average difference in distance traveled was 3.97 ± 3.37 mm. Overall, the HTC Vive shows promise as a tool for clinic, research, and industry and its controllers can be accurately tracked in a variety of situations. The methodology used for this study can easily be replicated for other VR systems so that direct comparisons can be made as new systems become available.     

The biology of ant-like jumping spiders (Araneae, Salticidae): prey and predatory behaviour of Myrtnarachne with particular attention to M. lupata from Queensland

Myrtnarachne is a genus of ant-like salticids. Eight species were observed feeding, in nature, in Australia, Kenya, Malaysia and Sri Lanka, on varied types of insects but not ants. The behaviour of M. lupata , from Australia, was studied in the laboratory. Predatory sequences were found to differ considerably from those of typical salticids. Attacking by lunging instead of leaping and the pronounced use of pre-attack tapping are especially noteworthy. The unusual behaviour of M. lupata when preying on insects is consistent with maintenance of ant mimicry. Myrmarachne lupata also preys on the eggs of other spiders which it extracts from their nests. The males of many species have very large chelicerae, and the large chelicerae of M. lupata males influence the course of predatory sequences, with insects and with eggs.     

Four-dimensional imaging with virtual reality to quantitatively explore jigsaw puzzle-like morphogenesis of Arabidopsis cotyledon pavement cells

In most dicotyledonous plants, leaf pavement cells exhibit complex jigsaw puzzle-like cell morphogenesis during leaf expansion. Although detailed molecular biological information and mathematical modeling of this jigsaw puzzle-like cell morphogenesis are now available, a full understanding of this process remains elusive. Recent reports have highlighted the importance of three-dimensional (3D) structures (i.e., anticlinal and periclinal cell wall) in understanding the mechanical models that describe this morphogenetic process. We believe that it is important to acquire 3D shapes of pavement cells over time, i.e., acquire and analyze four-dimensional (4D) information when studying the relationship between mechanical modeling and simulations and the actual cell shape. In this report, we have developed a framework to capture and analyze 4D morphological information of Arabidopsis thaliana cotyledon pavement cells by using both direct water immersion observations and computational image analyses, including segmentation, surface modeling, virtual reality and morphometry. The 4D cell models allowed us to perform time-lapse 3D morphometrical analysis, providing detailed quantitative information about changes in cell growth rate and shape, with cellular complexity observed to increase during cell growth. The framework should enable analysis of various phenotypes (e.g., mutants) in greater detail, especially in the 3D deformation of the cotyledon surface, and evaluation of theoretical models that describe pavement cell morphogenesis using computational simulations. Additionally, our accurate and high-throughput acquisition of growing cell structures should be suitable for use in generating in silico model cell structures.     

江西省跳蛛科蜘蛛区系及其与国内其他省、区异同比较

本文列出江西产跳蛛科蜘蛛30属63种的名录、地理分布以及区系特征。63种跳蛛属古北界的物种仅占6．2％,属东洋界以及东洋界、古北界共有物种分别占42．8％和51．0％。国内分布已基本查清的27种跳蛛区系分析表明：江西种类属华中区,与华南区、西南区共有种最多,其后依次为华北区、东北区、蒙新区,与青藏区共有种最少;江西跳蛛与邻省湖南共有种最多,其后依次为广东、福建、浙江、湖北、安徽,与江苏共有种最少。     

Mismatch between dietary requirements for lipid by a predator and availability of lipid in prey

Growth is an important factor in predicting an organism's overall success as an adult. Understanding how abiotic and biotic factors influence body size is key to predicting how environmental changes will impact organisms and predicting optimal behaviors under varying conditions. Food items can vary widely in nutrient content and this variation can affect growth. We tested how the quantity and macronutrient content of live prey affected the growth of juvenile jumping spiders, Phiddipus audax, using 420 spiderlings raised on one of 21 diets. In addition, we measured the nutrient content of prey from the field and compared average prey nutrient content with the diet at which spiders maximized growth. Our results show that the quantity and nutrient content of prey have significant and interacting effects on the growth of an actively hunting predator. In particular, spiders grew larger in body size (tibia/patella length and posterior lateral eye width) and were heavier on diets with higher lipid content. Yet, data on the nutrient content of prey from the field shows that most potential prey have high protein and low lipid content in their bodies. This apparent mismatch between spider nutritional requirements and prey nutrient availability likely presents a challenge to spiders seeking to maximize growth in the field. Several hypotheses for how these predators overcome this challenge to reach the large body sizes observed in the field are discussed.     

探索以“霍乱弧菌检测虚拟仿真实验”为载体的混合式实验教学模式

虚拟仿真实验是一种现代信息化和智慧教学的重要方法,对高等医学院校教学质量的发展起到重要的推进作用。我们自主开发建设的“霍乱弧菌检测与防控虚拟仿真实验”,既弥补了因生物安全问题不能开展的实验教学,也解决了微生物学检验实验教学中存在的操作标准化问题。采用“三步进阶”混合教学模式,实现以“学生为中心”的师生互动模式,创建“设计性实验报告”,与育人元素有机结合,培育医学生的职业使命感。细化考核标准,实现过程性评价。探索课前启发铺垫、课中内化升华、课后巩固拓展混合式实验教学模式,有效提高学生的实验技能,实现知行合一、素能共育的教学目标。