Developing the calcium-dependent conformational behavior of the RTX peptide domain for novel protein capture and recovery applications

The β-roll domain is a unique, conformationally dynamic peptide secondary structure motif1. This peptide is expressed from the repeats-in-toxin (RTX) domains found in some secreted pathogenic proteins. The peptide is intrinsically disordered in the absence of calcium. In calcium rich environments, the peptide binds Ca++ ions and folds into a β-roll secondary structure that resembles a flattened corkscrew. It is composed of two parallel β-sheet faces with a conserved aspartic acid at each turn that is responsible for the Ca++ binding. We have extensively characterized this calcium-responsive RTX domain and evaluated its potential as a new bioseparations platform in both non-chromatographic and affinity chromatography applications, as well as a novel component for the development of advanced protein hydrogels. We have developed a synthetic peptide, based on RTX domains, which undergoes calcium-responsive, reversible precipitation. This synthetic tag was appended to green fluorescent protein, β-lactamase and alcohol dehydrogenase. After protease cleavage of the precipitating tag, pure and active target proteins were obtained by cycling precipitation steps before and after cleavage. This work demonstrates a new stimulus-responsive precipitating tag that can be used for efficient bioseparations using gentler conditions than existing alternatives, enabling purification of recombinant proteins from microbial lysate in only a few minutes1. More recently, we have also shown that this β-roll peptide domain can serve as a new scaffold for engineering controllable biomolecular recognition. Mutant peptide libraries were selected against lysozyme via ribosome display and we were able to identify peptides with mid-nanomolar (63μM) dissociation constants. We showed that the mutant RTX peptides are capable of capturing the lysozyme target in affinity chromatography experiments in the presence of calcium and the bound target is easily eluted upon removal of the calcium ions, in a Catch and Release mechanism2. We have previously mutated the amino acids on the faces of the β-roll peptide domain to hydrophobic leucine side chains to enable calcium-induced self-assembly. This provides cross-links that enables calcium-dependent protein hydrogel formation4,5. We have introduced our lysozyme-binding β-roll peptide into this platform so that the designed proteins are a viscous liquid in the absence of calcium. Upon calcium addition, a robust hydrogel is formed that specifically binds the target protein, lysozyme6. Thus the engineering of the peptide domains has led to new biotechnology applications, where environmentally responsive protein hydrogels are capable of selective and reversible protein capture and immobilization. 1. Bulutoglu, B. and Banta, S. 2017 Toxins 9(9) 289. 2. Shur, O. et al. 2013, BioTechniques. 54(4): 197-206. 3. Bulutoglu, B. et al, 2017, ACS Syn Biol 6(9) 1732-1741. 4. Dooley, K., et al 2012, Biomacromol 13(6) 1758-1764. 5. Dooley, K. et al 2014, Biomacromol 15(10) 3617-3624. 6. Bulutoglu et al. 2017, Biomacromol 18(7) 2139-214

Predicting the Next Best View for 3D Mesh Refinement

3D reconstruction is a core task in many applications such as robot navigation or sites inspections. Finding the best poses to capture part of the scene is one of the most challenging topic that goes under the name of Next Best View. Recently, many volumetric methods have been proposed; they choose the Next Best View by reasoning over a 3D voxelized space and by finding which pose minimizes the uncertainty decoded into the voxels. Such methods are effective, but they do not scale well since the underlaying representation requires a huge amount of memory. In this paper we propose a novel mesh-based approach which focuses on the worst reconstructed region of the environment mesh. We define a photo-consistent index to evaluate the 3D mesh accuracy, and an energy function over the worst regions of the mesh which takes into account the mutual parallax with respect to the previous cameras, the angle of incidence of the viewing ray to the surface and the visibility of the region. We test our approach over a well known dataset and achieve state-of-the-art results.Comment: 13 pages, 5 figures, to be published in IAS-1

Estimating Turbulence Statistics and Parameters from Ground- and Nacelle-Based Lidar Measurements:IEA Wind Expert Report

The International Energy Agency Implementing Agreement for Co-operation in the Research, Development and Deployment of Wind Energy Systems (IEA Wind) is a vehicle for member countries to exchange information on the planning and execution of national, large-scale wind system projects and to undertake co-operative research and development projects called Tasks or Annexes. As a final result of research carried out in the IEA Wind Tasks, Recommended Practices, Best Practices, or Expert Group Reports may be issued. These documents have been developed and reviewed by experts in the specialized area they address. They have been reviewed and approved by participants in the research Task, and they have been reviewed and approved by the IEA Wind Executive Committee as guidelines useful in the development and deployment of wind energy systems. Use of these documents is completely voluntary. However, these documents are often adopted in part or in total by other standards-making bodies. A Recommended Practices document includes actions and procedures recommended by the experts involved in the research project. A Best Practices document includes suggested actions and procedures based on good industry practices collected during the research project. An Experts Group Studies report includes the latest background information on the topic as well as a survey of practices, where possible. Previously issued IEA Wind Recommended Practices, Best Practices, and Expert Group Reports can be found here on the Task 11 web pages

Sphingosine kinases and their metabolites modulate endolysosomal trafficking in photoreceptors

Alterations in sphingosine kinase activity change the degradation rates of Rhodopsin and the transient receptor potential (TRP) channel by lysosomes and can result in retinal degeneration

A single ubiquitin is sufficient for cargo protein entry into MVBs in the absence of ESCRT ubiquitination

While ESCRT-0 is ubiquitinated by the Rsp5 E3 ligase, loss of Rsp5 does not disrupt monoubiquitin-dependent sorting into multivesicular bodies

Identifying the need for good practices in Health Technology Assessment : summary of the ISPOR HTA Council Working Group Report on Good Practices in HTA

The systematic use of evidence to inform healthcare decisions, particularly health technology assessment (HTA), has gained increased recognition. HTA has become a standard policy tool for informing decision makers who must manage the entry and use of pharmaceuticals, medical devices, and other technologies (including complex interventions) within health systems, for example, through reimbursement and pricing. Despite increasing attention to HTA activities, there has been no attempt to comprehensively synthesize good practices or emerging good practices to support populationbased decision-making in recent years. After the identification of some good practices through the release of the ISPOR Guidelines Index in 2013, the ISPOR HTA Council identified a need to more thoroughly review existing guidance. The purpose of this effort was to create a basis for capacity building, education, and improved consistency in approaches to HTA-informed decision-making. Our findings suggest that although many good practices have been developed in areas of assessment and some other key aspects of defining HTA processes, there are also many areas where good practices are lacking. This includes good practices in defining the organizational aspects of HTA, the use of deliberative processes, and measuring the impact of HTA. The extent to which these good practices are used and applied by HTA bodies is beyond the scope of this report, but may be of interest to future researchers

Internet of Things in Sustainable Energy Systems

Our planet has abundant renewable and conventional energy resources but technological capability and capacity gaps coupled with water-energy needs limit the benefits of these resources to citizens. Through IoT technology solutions and state-of-the-art IoT sensing and communications approaches, the sustainable energy-related research and innovation can bring a revolution in this area. Moreover, by the leveraging current infrastructure, including renewable energy technologies, microgrids, and power-to-gas (P2G) hydrogen systems, the Internet of Things in sustainable energy systems can address challenges in energy security to the community, with a minimal trade-off to environment and culture. In this chapter, the IoT in sustainable energy systems approaches, methodologies, scenarios, and tools is presented with a detailed discussion of different sensing and communications techniques. This IoT approach in energy systems is envisioned to enhance the bidirectional interchange of network services in grid by using Internet of Things in grid that will result in enhanced system resilience, reliable data flow, and connectivity optimization. Moreover, the sustainable energy IoT research challenges and innovation opportunities are also discussed to address the complex energy needs of our community and promote a strong energy sector economy