Mobile Robot Team Forming for Crystallization of Proteins

The process of protein crystallization is explained using the theory of robotics, particularly path planning of mobile robots. Path planning is a procedure which specifies motion trajectories of multiple mobile robots to form a robotic team with a desired pattern. Since protein crystals consist of a large number of protein molecules which come together to form a 3D lattice of uniform structure, it is hypothesized that each protein behaves like a mobile robot and takes adequate path to form a robotic team (crystal). Based on this hypothesis, it is shown that trajectories of the proteins should be simple and local, which generates three rules of motion for the protein robots, i.e., a. each protein searches for its nearest neighbor, b. each protein takes the shortest path to approach the nearest neighbor, and c. multiple proteins may form a sub-team of proteins. It is then proven mathematically that the planned path according to the three rules is stable and able to crystallize the proteins. Interaction forces at the molecular level are analyzed to show that the simple and local motion of the proteins is physically warranted. Computer simulation and experimental results are presented to validate the new theory. Keywords Mobile robots, robot team forming, protein crystallization, simplicity and locality. 3/5/2007 draft 1 1

Protein crystal presentation for synchrotron methods:acoustic techniques

This thesis describes the design, development and testing of novel acoustic mounting methods for the diffraction of protein crystals for structural biology. Sample environment and presentation is a challenging field set within the larger subject of protein crystallography. The needs of researchers to achieve the highest resolution data collection from difficult to fabricate samples, sits alongside the need for complex experimental conditions, where temperature, hydration and chemistry must be altered and controlled. A movement within the structural biology field away from obtaining structures at cryogenic temperatures, towards high resolution structures at room temperature, where proteins may still function, has been the driver to search for novel solutions. To approach this ‘solution space’ the following work draws on acoustic manipulation techniques, looking for self-assembly and non-contact manipulation. Thus for the first time acoustic standing wave crystal trapping and also acoustically induced rotation have been shown in situ to be viable for use with protein crystallography, a fundamental proof paving the way for new time resolved and high throughput methods. The methods investigated included both surface acoustic and bulk acoustic waves, looking at self-assembly and flow induced rotation. Each demonstration addresses a fundamental need within the automation of room temperature crystallography, demonstrating both the technique and quantifying the diffraction resolution for the first time. Through the completion of these novel experiments acoustic sample presentation has been proven viable. The demonstrated method does not require crystals be removed from crystallisation fluid before mounting (using the acoustic trapping method), thus enabling the application of secondary fluids and paving the way for a fully continuous and microfluidic technology. Moreover acoustic goniometry lends itself to the automated mounting and collection of small batch crystal data by removing the need for delicate spine mounting. Both methods constitute a significant extension in the ability of researchers to utilise non-contact methods to control and interact with their proteins and crystals at room temperature

Workflow automation for image analysis of 2D crystals of membrane proteins

Membrane proteins carry out various functions essential to the survival of organ- isms. They transfer signals between the cell’s internal and external environments, move molecules and ions across the membrane, act as enzymes, and allow cell adhesion. This is why membrane proteins represent more than half of all drug targets. A deeper insight into the functional mechanisms of a protein can be gained from structural information. And so far only a fraction of membrane protein structures has been determined. The topic of this thesis is structure determination of membrane proteins through electron crystallography focusing on the image processing of 2D crystals. The thesis combines both method development and structure studies. In the Methods part, state of the art processing of 2D crystal images is presented. The workflow em- bedding all the processing steps from the initial micrographs of 2D crystals to the resulting 3D electron density map of the reconstituted membrane protein is de- scribed. The possibility of autonomous high-throughput processing is discussed as the ultimate goal of automation of this workflow. An additional processing step of the workflow that captures the variation of tilt geometry in the 2D crystal is introduced. This is implemented as an iterative refinement of the local tilt geometry using a Single Particle processing approach. A great benefit of electron crystallography is the fact that through reconstitution the purified protein is embedded in a natural environment, a membrane. Biochemical manipulations of this environment can lead to structural changes, which yields insight into the functional states of the protein. An new method of analyzing these structural changes in 2D projection maps is presented here. The method identifies significant changes in the protein by distinguishing them from noise derived artifacts. The second part of this thesis covers applications of these methods in structural studies of unknown membrane proteins. In the study of the Secondary Citrate/Sodium Symporter CitS, the substrate binding domain was identified with help of the significant difference map method. The improvements of the image processing routines were directly applied in the analysis of the 2D crystals. The structural studies of nucleotide-modulated potassium channel MloK1 also benefited from the automated image processing workflow and the significant difference map, while identifying structural changes through ligand binding. To gain a more detailed electron density map of MloK1, the local tilt geometry of the crystals were refined with the single particle 3D reconstruction for 2D crystal images method

Recent Advances in Multi Robot Systems

To design a team of robots which is able to perform given tasks is a great concern of many members of robotics community. There are many problems left to be solved in order to have the fully functional robot team. Robotics community is trying hard to solve such problems (navigation, task allocation, communication, adaptation, control, ...). This book represents the contributions of the top researchers in this field and will serve as a valuable tool for professionals in this interdisciplinary field. It is focused on the challenging issues of team architectures, vehicle learning and adaptation, heterogeneous group control and cooperation, task selection, dynamic autonomy, mixed initiative, and human and robot team interaction. The book consists of 16 chapters introducing both basic research and advanced developments. Topics covered include kinematics, dynamic analysis, accuracy, optimization design, modelling, simulation and control of multi robot systems

Development of a methodology linking protein phase behavior and Hydrophobic Interaction Chromatography

This thesis deals with the development of a universal methodology for the generation of protein phase diagrams in high-throughput in microbatch scale. The main influencing factors on binding behavior using Hydrophobic Interaction Chromatography (HIC) have been determined and new approaches for increasing binding capacity of HIC adsorbers have been developed. Additionally, fast tools have been investigated to predict binding behavior in HIC and to estimate protein phase behavior

Optimization and application of a flexible dual arm robot based automation system for sample preparation and measurement

This dissertation describes the optimization of the implementation of the Yaskawa SDA10F dual-arm robot to carry out routine sample preparation tasks in a life science laboratory such that standard lab equipment can be used and the robot can replace humans in sample preparation process. The existing robot control software is changed to carry out various tasks consecutively without interruption. Robot environment and motions were optimized allowing system expansion, multiple batches of samples are made at a time, increasing throughput. The system was validated with the help of two applications

Automation strategies for sample preparation in life science applications

Automation is broadly applied in life science field, with robots playing critical roles. In this dissertation, a platform based on a Yaskawa industrial dual-arm robot (CSDA10F) is presented, which is to automate the sample preparation processes and to integrate analytical instruments. A user-friendly interface has been provided by integrating the platform with SAMI Workstation EX Software. For automating the sample preparation processes, the robot needs to use various commercial tools, including pipette, syringe, microplate, vial, thermo shaker, ultrasonic machine and so on

Aerospace medicine and biology: A continuing bibliography with indexes (supplement 324)

This bibliography lists 200 reports, articles and other documents introduced into the NASA Scientific and Technical Information System during May, 1989. Subject coverage includes: aerospace medicine and psychology, life support systems and controlled environments, safety equipment, exobiology and extraterrestrial life, and flight crew behavior and performance

Nonterrestrial utilization of materials: Automated space manufacturing facility

Four areas related to the nonterrestrial use of materials are included: (1) material resources needed for feedstock in an orbital manufacturing facility, (2) required initial components of a nonterrestrial manufacturing facility, (3) growth and productive capability of such a facility, and (4) automation and robotics requirements of the facility

Large space structures and systems in the space station era: A bibliography with indexes (supplement 05)

Bibliographies and abstracts are listed for 1363 reports, articles, and other documents introduced into the NASA scientific and technical information system between January 1, 1991 and July 31, 1992. Topics covered include technology development and mission design according to system, interactive analysis and design, structural and thermal analysis and design, structural concepts and control systems, electronics, advanced materials, assembly concepts, propulsion and solar power satellite systems