Regulatory mechanism of the light-activable allosteric switch LOV-TAP for the control of DNA binding: a computer simulation study

The spatio-temporal control of gene expression is fundamental to elucidate cell proliferation and deregulation phenomena in living systems. Novel approaches based on light-sensitive multiprotein complexes have recently been devised, showing promising perspectives for the noninvasive and reversible modulation of the DNA-transcriptional activity in vivo. This has lately been demonstrated in a striking way through the generation of the artificial protein construct light-oxygen-voltage (LOV)-tryptophan-activated protein (TAP), in which the LOV-2-Jα photoswitch of phototropin1 from Avena sativa (AsLOV2-Jα) has been ligated to the tryptophan-repressor (TrpR) protein from Escherichia coli. Although tremendous progress has been achieved on the generation of such protein constructs, a detailed understanding of their functioning as opto-genetical tools is still in its infancy. Here, we elucidate the early stages of the light-induced regulatory mechanism of LOV-TAP at the molecular level, using the noninvasive molecular dynamics simulation technique. More specifically, we find that Cys450-FMN-adduct formation in the AsLOV2-Jα-binding pocket after photoexcitation induces the cleavage of the peripheral Jα-helix from the LOV core, causing a change of its polarity and electrostatic attraction of the photoswitch onto the DNA surface. This goes along with the flexibilization through unfolding of a hairpin-like helix-loop-helix region interlinking the AsLOV2-Jα- and TrpR-domains, ultimately enabling the condensation of LOV-TAP onto the DNA surface. By contrast, in the dark state the AsLOV2-Jα photoswitch remains inactive and exerts a repulsive electrostatic force on the DNA surface. This leads to a distortion of the hairpin region, which finally relieves its tension by causing the disruption of LOV-TAP from the DNA.

The foundations of computer assisted surgery

Using navigation systems in general orthopaedic surgery and, in particular, knee replacement is becoming more and more accepted. This paper describes the basic technological concepts of modern computer assisted surgical systems. It explains the variation in currently available systems and outlines research activities that will potentially influence future products. In general, each navigation system is defined by three components: (1) the therapeutic object is the anatomical structure that is operated on using the navigation system, (2) the virtual object represents an image of the therapeutic object, with radiological images or computer generated models potentially being used, and (3) last but not least, the navigator acquires the spatial position and orientation of instruments and anatomy thus providing the necessary data to replay surgical action in real-time on the navigation system's screen.

Prosthetically driven, computer-guided implant planning for the edentulous maxilla: a model study

OBJECTIVES: To analyze computer-assisted diagnostics and virtual implant planning and to evaluate the indication for template-guided flapless surgery and immediate loading in the rehabilitation of the edentulous maxilla. MATERIALS AND METHODS: Forty patients with an edentulous maxilla were selected for this study. The three-dimensional analysis and virtual implant planning was performed with the NobelGuide software program (Nobel Biocare, Göteborg, Sweden). Prior to the computer tomography aesthetics and functional aspects were checked clinically. Either a well-fitting denture or an optimized prosthetic setup was used and then converted to a radiographic template. This allowed for a computer-guided analysis of the jaw together with the prosthesis. Accordingly, the best implant position was determined in relation to the bone structure and prospective tooth position. For all jaws, the hypothetical indication for (1) four implants with a bar overdenture and (2) six implants with a simple fixed prosthesis were planned. The planning of the optimized implant position was then analyzed as follows: the number of implants was calculated that could be placed in sufficient quantity of bone. Additional surgical procedures (guided bone regeneration, sinus floor elevation) that would be necessary due the reduced bone quality and quantity were identified. The indication of template-guided, flapless surgery or an immediate loaded protocol was evaluated. RESULTS: Model (a) - bar overdentures: for 28 patients (70%), all four implants could be placed in sufficient bone (total 112 implants). Thus, a full, flapless procedure could be suggested. For six patients (15%), sufficient bone was not available for any of their planned implants. The remaining six patients had exhibited a combination of sufficient or insufficient bone. Model (b) - simple fixed prosthesis: for 12 patients (30%), all six implants could be placed in sufficient bone (total 72 implants). Thus, a full, flapless procedure could be suggested. For seven patients (17%), sufficient bone was not available for any of their planned implants. The remaining 21 patients had exhibited a combination of sufficient or insufficient bone. DISCUSSION: In the maxilla, advanced atrophy is often observed, and implant placement becomes difficult or impossible. Thus, flapless surgery or an immediate loading protocol can be performed just in a selected number of patients. Nevertheless, the use of a computer program for prosthetically driven implant planning is highly efficient and safe. The three-dimensional view of the maxilla allows the determination of the best implant position, the optimization of the implant axis, and the definition of the best surgical and prosthetic solution for the patient. Thus, a protocol that combines a computer-guided technique with conventional surgical procedures becomes a promising option, which needs to be further evaluated and improved.

Mechanisms of Ligand–Protein Interaction in Sec-14-like Transporters Investigated by Computer Simulations

We review our recent work on protein-ligand interactions in vitamin transporters of the Sec-14-like protein. Our studies focused on the cellular-retinaldehyde binding protein (CRALBP) and the alpha-tocopherol transfer protein (alpha-TTP). CRALBP is responsible for mobilisation and photo-protection of short-chain cis-retinoids in the dim-light visual cycle or rod photoreceptors. alpha-TTP is a key protein responsible for selection and retention of RRR-alpha-tocopherol, the most active isoform of vitamin E in superior animals. Our simulation studies evidence how subtle chemical variations in the substrate can lead to significant distortion in the structure of the complex, and how these changes can either lead to new protein function, or be used to model engineered protein variants with tailored properties. Finally, we show how integration of computational and experimental results can contribute in synergy to the understanding of fundamental processes at the biomolecular scale.

Fully Automatic CT Segmentation for Computer-Assisted Pre-operative Planning of Hip Arthroscopy

Extraction of both pelvic and femoral surface models of a hip joint from CT data for computer-assisted pre-operative planning of hip arthroscopy is addressed. We present a method for a fully automatic image segmentation of a hip joint. Our method works by combining fast random forest (RF) regression based landmark detection, atlas-based segmentation, with articulated statistical shape model (aSSM) based hip joint reconstruction. The two fundamental contributions of our method are: (1) An improved fast Gaussian transform (IFGT) is used within the RF regression framework for a fast and accurate landmark detection, which then allows for a fully automatic initialization of the atlas-based segmentation; and (2) aSSM based fitting is used to preserve hip joint structure and to avoid penetration between the pelvic and femoral models. Validation on 30 hip CT images show that our method achieves high performance in segmenting pelvis, left proximal femur, and right proximal femur surfaces with an average accuracy of 0.59 mm, 0.62 mm, and 0.58 mm, respectively.

Knowledge-Based Task Structure Planning for an Information Gathering Agent

An effective solution to model and apply planning domain knowledge for deliberation and action in probabilistic, agent-oriented control is presented. Specifically, the addition of a task structure planning component and supporting components to an agent-oriented architecture and agent implementation is described. For agent control in risky or uncertain environments, an approach and method of goal reduction to task plan sets and schedules of action is presented. Additionally, some issues related to component-wise, situation-dependent control of a task planning agent that schedules its tasks separately from planning them are motivated and discussed.

Cerebellar mechanisms for motor learning: Testing predictions from a large-scale computer simulation

The cerebellum is the major brain structure that contributes to our ability to improve movements through learning and experience. We have combined computer simulations with behavioral and lesion studies to investigate how modification of synaptic strength at two different sites within the cerebellum contributes to a simple form of motor learning—Pavlovian conditioning of the eyelid response. These studies are based on the wealth of knowledge about the intrinsic circuitry and physiology of the cerebellum and the straightforward manner in which this circuitry is engaged during eyelid conditioning. Thus, our simulations are constrained by the well-characterized synaptic organization of the cerebellum and further, the activity of cerebellar inputs during simulated eyelid conditioning is based on existing recording data. These simulations have allowed us to make two important predictions regarding the mechanisms underlying cerebellar function, which we have tested and confirmed with behavioral studies. The first prediction describes the mechanisms by which one of the sites of synaptic modification, the granule to Purkinje cell synapses (gr → Pkj) of the cerebellar cortex, could generate two time-dependent properties of eyelid conditioning—response timing and the ISI function. An empirical test of this prediction using small, electrolytic lesions of the cerebellar cortex revealed the pattern of results predicted by the simulations. The second prediction made by the simulations is that modification of synaptic strength at the other site of plasticity, the mossy fiber to deep nuclei synapses (mf → nuc), is under the control of Purkinje cell activity. The analysis predicts that this property should confer mf → nuc synapses with resistance to extinction. Thus, while extinction processes erase plasticity at the first site, residual plasticity at mf → nuc synapses remains. The residual plasticity at the mf → nuc site confers the cerebellum with the capability for rapid relearning long after the learned behavior has been extinguished. We confirmed this prediction using a lesion technique that reversibly disconnected the cerebellar cortex at various stages during extinction and reacquisition of eyelid responses. The results of these studies represent significant progress toward a complete understanding of how the cerebellum contributes to motor learning. ^

Advanced Protein Modeling Method: Benchmarking and Applications in Computer-Aided Drug Discovery

Development of homology modeling methods will remain an area of active research. These methods aim to develop and model increasingly accurate three-dimensional structures of yet uncrystallized therapeutically relevant proteins e.g. Class A G-Protein Coupled Receptors. Incorporating protein flexibility is one way to achieve this goal. Here, I will discuss the enhancement and validation of the ligand-steered modeling, originally developed by Dr. Claudio Cavasotto, via cross modeling of the newly crystallized GPCR structures. This method uses known ligands and known experimental information to optimize relevant protein binding sites by incorporating protein flexibility. The ligand-steered models were able to model, reasonably reproduce binding sites and the co-crystallized native ligand poses of the β2 adrenergic and Adenosine 2A receptors using a single template structure. They also performed better than the choice of template, and crude models in a small scale high-throughput docking experiments and compound selectivity studies. Next, the application of this method to develop high-quality homology models of Cannabinoid Receptor 2, an emerging non-psychotic pain management target, is discussed. These models were validated by their ability to rationalize structure activity relationship data of two, inverse agonist and agonist, series of compounds. The method was also applied to improve the virtual screening performance of the β2 adrenergic crystal structure by optimizing the binding site using β2 specific compounds. These results show the feasibility of optimizing only the pharmacologically relevant protein binding sites and applicability to structure-based drug design projects.

Decomposition of $\rm R\times C$ contingency table chi -square: Application to binned DNA fragment size data and population structure analysis

The purpose of this research is to develop a new statistical method to determine the minimum set of rows (R) in a R x C contingency table of discrete data that explains the dependence of observations. The statistical power of the method will be empirically determined by computer simulation to judge its efficiency over the presently existing methods. The method will be applied to data on DNA fragment length variation at six VNTR loci in over 72 populations from five major racial groups of human (total sample size is over 15,000 individuals; each sample having at least 50 individuals). DNA fragment lengths grouped in bins will form the basis of studying inter-population DNA variation within the racial groups are significant, will provide a rigorous re-binning procedure for forensic computation of DNA profile frequencies that takes into account intra-racial DNA variation among populations. ^

Integrated learning of computer applications for production engineering

A high productivity rate in Engineering is related to an efficient management of the flow of the large quantities of information and associated decision making activities that are consubstantial to the Engineering processes both in design and production contexts. Dealing with such problems from an integrated point of view and mimicking real scenarios is not given much attention in Engineering degrees. In the context of Engineering Education, there are a number of courses designed for developing specific competencies, as required by the academic curricula, but not that many in which integration competencies are the main target. In this paper, a course devoted to that aim is discussed. The course is taught in a Marine Engineering degree but the philosophy could be used in any Engineering field. All the lessons are given in a computer room in which every student can use each all the treated software applications. The first part of the course is dedicated to Project Management: the students acquire skills in defining, using Ms-PROJECT, the work breakdown structure (WBS), and the organization breakdown structure (OBS) in Engineering projects, through a series of examples of increasing complexity, ending up with the case of vessel construction. The second part of the course is dedicated to the use of a database manager, Ms-ACCESS, for managing production related information. A series of increasing complexity examples is treated ending up with the management of the pipe database of a real vessel. This database consists of a few thousand of pipes, for which a production timing frame is defined, which connects this part of the course with the first one. Finally, the third part of the course is devoted to the work with FORAN, an Engineering Production package of widespread use in the shipbuilding industry. With this package, the frames and plates where all the outfitting will be carried out are defined through cooperative work by the studens, working simultaneously in the same 3D model. In the paper, specific details about the learning process are given. Surveys have been posed to the students in order to get feed-back from their experience as well as to assess their satisfaction with the learning process. Results from these surveys are discussed in the paper

3D hp-adaptive finite element simulations of a magic-T electromagnetic waveguide structure

This paper employs a 3D hp self-adaptive grid-refinement finite element strategy for the solution of a particular electromagnetic waveguide structure known as Magic-T. This structure is utilized as a power divider/combiner in communication systems as well as in other applications. It often incorporates dielectrics, metallic screws, round corners, and so on, which may facilitate its construction or improve its design, but significantly difficult its modeling when employing semi-analytical techniques. The hp-adaptive finite element method enables accurate modeling of a Magic-T structure even in the presence of these undesired materials/geometries. Numerical results demonstrate the suitability of the hp-adaptive method for modeling a Magic-T rectangular waveguide structure, delivering errors below 0.5% with a limited number of unknowns. Solutions of waveguide problems delivered by the self-adaptive hp-FEM are comparable to those obtained with semi-analytical techniques such as the Mode Matching method, for problems where the latest methods can be applied. At the same time, the hp-adaptive FEM enables accurate modeling of more complex waveguide structures.

SVis: A computational steering visualization environment for surface structure determination

The arrangement of atoms at the surface of a solid accounts for many of its properties: Hardness, chemical activity, corrosion, etc. are dictated by the precise surface structure. Hence, finding it, has a broad range of technical and industrial applications. The ability to solve this problem opens the possibility of designing by computer materials with properties tailored to specific applications. Since the search space grows exponentially with the number of atoms, its solution cannot be achieved for arbitrarily large structures. Presently, a trial and error procedure is used: an expert proposes an structure as a candidate solution and tries a local optimization procedure on it. The solution relaxes to the local minimum in the attractor basin corresponding to the initial point, that might be the one corresponding to the global minimum or not. This procedure is very time consuming and, for reasonably sized surfaces, can take many iterations and much effort from the expert. Here we report on a visualization environment designed to steer this process in an attempt to solve bigger structures and reduce the time needed. The idea is to use an immersive environment to interact with the computation. It has immediate feedback to assess the quality of the proposed structure in order to let the expert explore the space of candidate solutions. The visualization environment is also able to communicate with the de facto local solver used for this problem. The user is then able to send trial structures to the local minimizer and track its progress as they approach the minimum. This allows for simultaneous testing of candidate structures. The system has also proved very useful as an educational tool for the field.

Theoretical Simulation of the A5 VEB Structure Pyrotechnique Shock Propagation

This paper presents some of the modelling criteria that have been used for the study of pyrotechnic shock propagation in the A5 VEB Structure, as well as the main conclusions from a mathematical model of the axymmetric effects in it. The separation of the lower stage of the ARIANE 5 Vehicle Equipment Bay (VEB)Structure is to be done using a pyrotechnic device. The wave propagation effects produced by the explosion have been analyzed with a computer program using as shape functions the analytical solution to the frequency response of a Timoshenko-Rayleigh beams and shells in that way the discretization can have elements as large as possible, depending on the material properties and boundary conditions. Moreover an enormous amount of possibilities in the treatment of concentrated masses, springs and dashpots, either with respect to a fixed reference or between nodes, is open for translational as well as rotational degrees of freedom.