Modeling and optimization of rotational C-arm stereoscopic X-ray angiography

Investigation of the effect of UV-B light on Arabidopsis MYB4 (AtMYB4) transcription factor stability and detection of a putative MYB4-binding motif in the promoter proximal region of AtMYB4

Here, we have investigated the possible effect of UV-B light on the folding/unfolding properties and stability of Arabidopsis thaliana MYB4 (AtMYB4) transcription factor in vitro by using biophysical approaches. Urea-induced equilibrium unfolding analyses have shown relatively higher stability of the wild-type recombinant AtMYB4 protein than the N-terminal deletion forms after UV-B exposure. However, as compared to wild-type form, AtMYB4Δ2 protein, lacking both the two N-terminal MYB domains, showed appreciable alteration in the secondary structure following UV-B exposure. UV-B irradiated AtMYB4Δ2 also displayed higher propensity of aggregation in light scattering experiments, indicating importance of the N-terminal modules in regulating the stability of AtMYB4 under UV-B stress. DNA binding assays have indicated specific binding activity of AtMYB4 to a putative MYB4 binding motif located about 212 bp upstream relative to transcription start site of AtMYB4 gene promoter, while relatively weak DNA binding activity was detected for another putative MYB4 motif located at -908 bp in AtMYB4 promoter. Gel shift and fluorescence anisotropy studies have shown increased binding affinity of UV-B exposed AtMYB4 to the promoter proximal MYB4 motif. ChIP assay has revealed binding of AtMYB4 to the promoter proximal (-212 position) MYB4 motif (ACCAAAC) in vivo. Docking experiments further revealed mechanistic detail of AtMYB4 interaction with the putative binding motifs. Overall, our results have indicated that the N-terminal 62–116 amino acid residues constituting the second MYB domain plays an important role in maintaining the stability of the C-terminal region and the overall stability of the protein, while a promoter proximal MYB-motif in AtMYB4 promoter may involve in the regulation of its own expression under UV-B light.

Protein Structure Prediction Using Homology Modeling

Sequence-structure deficit marks one of the critical problems in today's scenario where high-throughput sequencing has resulted in large datasets of protein sequences but their corresponding 3D structures still needs to be determined. Homology modeling, also termed as Comparative modeling refers to modeling of 3D structure of a protein by exploiting structural information from other known protein structures with good sequence similarity. Homology models contain sufficient information about the spatial arrangement of important residues in the protein and are often used in drug design for screening of large libraries by molecular docking techniques. This chapter provides a brief description about protein tertiary structure prediction and Homology modeling. The authors provide a description of the steps involved in homology modeling protocols and provide information on the various resources available for the same.

Antiviral Compounds Against Nucleocapsid Protein of Porcine Epidemic Diarrhea Virus

Porcine epidemic diarrhea (PED) is a severe diarrhea disease in swine that is caused by porcine epidemic diarrhea virus (PEDV). Nucleocapsid (N) protein is the RNA-binding protein of PEDV, which plays an important role for virus life cycle. The aim of this research was to screen and characterize the compounds that could inhibit the activity of PEDV N protein. The gene encoding PEDV N protein obtained from PEDV Thai isolate was cloned and expressed in E. coli. Its amino acid sequence was employed to generate the three dimensional structure by homology modeling. There were 1,286 compounds of FDA-approved drug database that could virtually bind to the RNA-binding region of N protein. Three compounds, trichlormethiazide, D-(+) biotin, and glutathione successfully bound to the N protein, in vitro, with the IC₅₀ at 8.754 mg/mL, 0.925 mg/mL, and 2.722 mg/mL. Antiviral activity in PEDV-infected Vero cells demonstrated that the effective concentration of trichlormethiazide, D-(+) biotin, and glutathione in inhibiting PEDV replication were 0.094, 0.094 and 1.5 mg/mL. This study demonstrated a strategy applied for discovery of antiviral agents capable of inhibiting PEDV N protein and PEDV replication. The compounds identified here exhibited a potential use as therapeutic agents for controlling PEDV infection.

Accurate micro-computed tomography imaging of pore spaces in collagen-based scaffold

In this work we have used X-ray micro-computed tomography (μCT) as a method to observe the morphology of 3D porous pure collagen and collagen-composite scaffolds useful in tissue engineering. Two aspects of visualizations were taken into consideration: improvement of the scan and investigation of its sensitivity to the scan parameters. Due to the low material density some parts of collagen scaffolds are invisible in a μCT scan. Therefore, here we present different contrast agents, which increase the contrast of the scanned biopolymeric sample for μCT visualization. The increase of contrast of collagenous scaffolds was performed with ceramic hydroxyapatite microparticles (HAp), silver ions (Ag(+)) and silver nanoparticles (Ag-NPs). Since a relatively small change in imaging parameters (e.g. in 3D volume rendering, threshold value and μCT acquisition conditions) leads to a completely different visualized pattern, we have optimized these parameters to obtain the most realistic picture for visual and qualitative evaluation of the biopolymeric scaffold. Moreover, scaffold images were stereoscopically visualized in order to better see the 3D biopolymer composite scaffold morphology. However, the optimized visualization has some discontinuities in zoomed view, which can be problematic for further analysis of interconnected pores by commonly used numerical methods. Therefore, we applied the locally adaptive method to solve discontinuities issue. The combination of contrast agent and imaging techniques presented in this paper help us to better understand the structure and morphology of the biopolymeric scaffold that is crucial in the design of new biomaterials useful in tissue engineering.

Homology modeling a fast tool for drug discovery: current perspectives

Major goal of structural biology involve formation of protein-ligand complexes; in which the protein molecules act energetically in the course of binding. Therefore, perceptive of protein-ligand interaction will be very important for structure based drug design. Lack of knowledge of 3D structures has hindered efforts to understand the binding specificities of ligands with protein. With increasing in modeling software and the growing number of known protein structures, homology modeling is rapidly becoming the method of choice for obtaining 3D coordinates of proteins. Homology modeling is a representation of the similarity of environmental residues at topologically corresponding positions in the reference proteins. In the absence of experimental data, model building on the basis of a known 3D structure of a homologous protein is at present the only reliable method to obtain the structural information. Knowledge of the 3D structures of proteins provides invaluable insights into the molecular basis of their functions. The recent advances in homology modeling, particularly in detecting and aligning sequences with template structures, distant homologues, modeling of loops and side chains as well as detecting errors in a model contributed to consistent prediction of protein structure, which was not possible even several years ago. This review focused on the features and a role of homology modeling in predicting protein structure and described current developments in this field with victorious applications at the different stages of the drug design and discovery.

Full-scale 3D preoperative planning system for calcaneal osteotomy with a multimedia system

This study presents a new computer-assisted surgical planning and simulating system that employs a multimedia environment for calcaneal osteotomy surgery. The system uses a full-scale computer-assisted engineering technique for designing and developing preoperative planning modules. The planning system not only presents a real-sized 3-dimensional (3D) image of the calcaneus, but also provides detailed interior measurements of the calcaneus from various cutting planes. The multimedia user interface integrates the function of different software programs in order to plan and simulate the operation. These functions include 3D image model capturing, sectioning, translocation, rotating, and measuring relevant foot anatomy, all of which can be integrated and used for surgical planning, as well as for future study and discussion. Furthermore, because the system is computer based with a multimedia user interface, surgeons can use it to explore the optimal operative procedure. The system also has a databank that can be updated and expanded, and can be used to provide clinical cases to different users for education and training.

LEVEL OF CLINICAL EVIDENCE

5.

Rotational roadmapping: a new image-based navigation technique for the interventional room

For decades, conventional 2D-roadmaping has been the method of choice for image-based guidewire navigation during endovascular procedures. Only recently have 3D-roadmapping techniques become available that are based on the acquisition and reconstruction of a 3D image of the vascular tree. In this paper, we present a new image-based navigation technique called RoRo (Rotational Roadmapping) that eliminates the guess-work inherent to the conventional 2D method, but does not require a 3D image. Our preliminary clinical results show that there are situations in which RoRo is preferred over the existing two methods, thus demonstrating potential for filling a clinical niche and complementing the spectrum of available navigation tools.

Advances in homology protein structure modeling

Homology modeling plays a central role in determining protein structure in the structural genomics project. The importance of homology modeling has been steadily increasing because of the large gap that exists between the overwhelming number of available protein sequences and experimentally solved protein structures, and also, more importantly, because of the increasing reliability and accuracy of the method. In fact, a protein sequence with over 30% identity to a known structure can often be predicted with an accuracy equivalent to a low-resolution X-ray structure. The recent advances in homology modeling, especially in detecting distant homologues, aligning sequences with template structures, modeling of loops and side chains, as well as detecting errors in a model, have contributed to reliable prediction of protein structure, which was not possible even several years ago. The ongoing efforts in solving protein structures, which can be time-consuming and often difficult, will continue to spur the development of a host of new computational methods that can fill in the gap and further contribute to understanding the relationship between protein structure and function.

Technology and Perception in the 21st-Century Reading Room

Radiology reading rooms have changed dramatically over the past 15 years, moving from analog-light-box-based environments to digital-display-based environments. Most of the focus in the early stages of this transition was on the technology, but it soon became obvious that it was not possible or even prudent to consider the technology without considering radiologists. The information being presented to radiologists in digital reading rooms is in many ways very different from that presented on traditional film. On one hand, the digital workstation display medium itself is very different from traditional film images hung on light boxes. On the other hand, without large-area light boxes, images such as those from computed tomography (CT) can no longer be displayed all at once in a series of film sheets. The digital world also introduces the possibility of manipulating image data in ways that were never possible with analog film. Not only can radiologists manipulate image data with various image-processing tools, but also, computers can analyze images and provide even more information to incorporate into the interpretation process. As a consequence of these differences, it has been necessary to focus attention on radiologists to discover ways to optimize the digital reading environment with respect to the human visual system and the way the eye-brain system processes information. This article reviews some of the important perceptual issues that have arisen in the digital reading rooms of the 21st century.

A global method based on thin-plate splines for correction of geometric distortion: an application to fluoroscopic images

Quantitative analysis of biomedical images needs a careful correction of geometric distortion. To avoid the discontinuities of the local correction techniques and achieve good accuracy in the presence of global and local distortion, a novel global correction technique based on thin-plate splines is proposed. The technique approximates the grid points by a thin plate minimizing the weighted sum of the bending energy and the mean squared residual errors. The method proposed is compared with three traditional correction techniques: two local and one global. One local technique is linear and takes into account translation, rotation, and scaling, the other is nonlinear and includes skewing. The global technique is based on a two-dimensional polynomial model. Computer-based simulations and experimental tests on fluoroscopic images were carried out. The local techniques were sensitive to both sigmoidal and radial distortion. The polynomial and thin-plate splines global techniques were found sensitive only to sigmoidal distortion and to radial distortion, respectively. The two global techniques showed better performances with respect to any local on synthetic and real images. Where the distortion is predominantly radial or high computational efficiency is required, the polynomial global correction technique should be preferred. Where the distortion has a local nature or is predominantly sigmoidal, the thin-plate splines global correction technique should be chosen.

A method for correction of radiographic errors in serial three-dimensional cephalometry

OBJECTIVES

To improve the accuracy of location of anatomical structures in serial three-dimensional (3D) cephalometric radiography.

METHODS

A new method was developed to correct for geometrical errors in the calculation of the 3D coordinates of a point viewed on any two of three frontal, lateral and axial cephalometric radiographs. A computer-based method was used to reduce measurement errors. The methods were tested on a phantom containing metallic markers and on a dried skull.

RESULTS

The mean corrected geometric error was 0.43 mm (SD 0.25 mm) compared with a maximum of 8 mm (SD 0.2 mm) when calculated directly from the radiographs. The mean computer-based measurement error was 0.46 mm (SD 0.34 mm) compared with 1.38 mm (SD 0.74 mm) when made directly from the radiographs.

CONCLUSIONS

The new method for the correction of radiographic errors in 3D serial cephalometric radiography appears to be sufficiently accurate to justify clinical evaluation.