Recent Developments in Data-Assisted Modeling of Flexible Proteins

Many proteins can fold into well-defined conformations. However, intrinsically-disordered proteins (IDPs) do not possess a defined structure. Moreover, folded multi-domain proteins often digress into alternative conformations. Collectively, the conformational dynamics enables these proteins to fulfill specific functions. Thus, most experimental observables are averaged over the conformations that constitute an ensemble. In this article, we review the recent developments in the concept and methods for the determination of the dynamic structures of flexible peptides and proteins. In particular, we describe ways to extract information from nuclear magnetic resonance small-angle X-ray scattering (SAXS), and chemical cross-linking coupled with mass spectroscopy (XL-MS) measurements. All these techniques can be used to obtain ensemble-averaged restraints or to re-weight the simulated conformational ensembles.

Lipid Droplets, Phospholipase A2, Arachidonic Acid, and Atherosclerosis

Lipid droplets, classically regarded as static storage organelles, are currently considered as dynamic structures involved in key processes of lipid metabolism, cellular homeostasis and signaling. Studies on the inflammatory state of atherosclerotic plaques suggest that circulating monocytes interact with products released by endothelial cells and may acquire a foamy phenotype before crossing the endothelial barrier and differentiating into macrophages. One such compound released in significant amounts into the bloodstream is arachidonic acid, the common precursor of eicosanoids, and a potent inducer of neutral lipid synthesis and lipid droplet formation in circulating monocytes. Members of the family of phospholipase A2, which hydrolyze the fatty acid present at the sn-2 position of phospholipids, have recently emerged as key controllers of lipid droplet homeostasis, regulating their formation and the availability of fatty acids for lipid mediator production. In this paper we discuss recent findings related to lipid droplet dynamics in immune cells and the ways these organelles are involved in regulating arachidonic acid availability and metabolism in the context of atherosclerosis.

Stomata Detector: High-throughput automation of stomata counting in a population of African rice (Oryza glaberrima) using transfer learning

Stomata are dynamic structures that control the gaseous exchange of CO2 from the external to internal environment and water loss through transpiration. The density and morphology of stomata have important consequences in crop productivity and water use efficiency, both are integral considerations when breeding climate change resilient crops. The phenotyping of stomata is a slow manual process and provides a substantial bottleneck when characterising phenotypic and genetic variation for crop improvement. There are currently no open-source methods to automate stomatal counting. We used 380 human annotated micrographs of O. glaberrima and O. sativa at x20 and x40 objectives for testing and training. Training was completed using the transfer learning for deep neural networks method and R-CNN object detection model. At a x40 objective our method was able to accurately detect stomata (n = 540, r = 0.94, p<0.0001), with an overall similarity of 99% between human and automated counting methods. Our method can batch process large files of images. As proof of concept, characterised the stomatal density in a population of 155 O. glaberrima accessions, using 13,100 micrographs. Here, we present developed Stomata Detector; an open source, sophisticated piece of software for the plant science community that can accurately identify stomata in Oryza spp., and potentially other monocot species.

Predicate-Based Model of Problem-Solving for Robotic Actions Planning

The aim of the article is to describe a predicate-based logical model for the problem-solving of robots. The proposed article deals with analyses of trends of problem-solving robotic applications for manufacturing, especially for transportations and manipulations. Intelligent agent-based manufacturing systems with robotic agents are observed. The intelligent cores of them are considered from point of view of ability to propose the plans of problem-solving in the form of strategies. The logical model of adaptive strategies planning for the intelligent robotic system is composed in the form of predicates with a presentation of data processing on a base of set theory. The dynamic structures of workspaces, and a possible change of goals are considered as reasons for functional strategies adaptation.

Delivery of nanovaccine towards lymphoid organs: recent strategies in enhancing cancer immunotherapy

With the in-depth exploration on cancer therapeutic nanovaccines, increasing evidence shows that the poor delivery of nanovaccines to lymphoid organs has become the culprit limiting the rapid induction of anti-tumor immune response. Unlike the conventional prophylactic vaccines that mainly form a depot at the injection site to gradually trigger durable immune response, the rapid proliferation of tumors requires an efficient delivery of nanovaccines to lymphoid organs for rapid induction of anti-tumor immunity. Optimization of the physicochemical properties of nanovaccine (e.g., size, shape, charge, colloidal stability and surface ligands) is an effective strategy to enhance their accumulation in lymphoid organs, and nanovaccines with dynamic structures are also designed for precise targeted delivery of lymphoid organs or their subregions. The recent progress of these nanovaccine delivery strategies is highlighted in this review, and the challenges and future direction are also discussed. Graphical Abstract

Function of Centriolar Satellites and Regulation by Post-Translational Modifications

Centriolar satellites are small membrane-less granules that gravitate around the centrosome. Recent advances in defining the satellite proteome and interactome have unveiled hundreds of new satellite components thus illustrating the complex nature of these particles. Although initially linked to the homeostasis of centrosome and the formation of primary cilia, these composite and highly dynamic structures appear to participate in additional cellular processes, such as proteostasis, autophagy, and cellular stress. In this review, we first outline the main features and many roles of centriolar satellites. We then discuss how post-translational modifications, such as phosphorylation and ubiquitination, shape their composition and functions. This is of particular interest as interfering with these processes may provide ways to manipulate these structures.