ABSTRACT
Background: Although Charcot diabetic foot (CDF) is a frequent complication of diabetic neuropathy, less is known about the possibility of its early prevention. Methods: A review of the original articles published in English, using the "biomarkers AND Charcot's foot" criterion, resulted in 33 articles from the PubMed database and seven articles from the Web of Science database. The five duplicates were eliminated, and two independent reviewers selected the most relevant articles, leaving a total of 21 articles. Results: The biomarkers identified are exhaustively described, related to the system of advanced glycation end products (AGEs) and their soluble receptors (sRAGE), inflammatory cascade, osteoclastogenesis, and, respectively, osteoblastic activity. Conclusions: This article highlights the importance of potential early identifiable biomarkers that can lead to microstructural changes in the affected bones.
ABSTRACT
Rapid and specific detection of extended-spectrum ß-lactamase-producing (ESBL) bacteria is crucial both for timely antibiotic therapy when treating infected patients as well as for appropriate infection control measures aimed at curbing the spread of ESBL-producing isolates. Whereas a variety of phenotypic methods are currently available for ESBL detection, they remain time consuming and sometimes difficult to interpret while being also affected by a lack of sensitivity and specificity. Considering the longer turnaround time (TAT) of susceptibility testing and culture results, DNA-based ESBL identification would be a valuable surrogate for phenotypic-based methods. Putative ESBL-positive Enterobacteriaceae isolates (n = 330) from clinical specimen were prospectively collected in Bulgaria, Romania and Democratic Republic of Congo and tested in this study. All isolates were assessed for ESBL-production by the E-test method and those giving undetermined ESBL status were re-tested using the combination disk test. A genotypic assay successively combining qPCR detection of blaCTX-M, blaTEM and blaSHV genes with a multiplex pyrosequencing of blaTEM and blaSHV genes was developed in order to detect the most common ESBL-associated TEM and SHV single nucleotides polymorphisms, irrespective of their plasmid and/or chromosomal location. This assay was applied on all Enterobacteriaceae isolates (n = 330). Phenotypic and genotypic results matched in 324/330 (98.2%). Accordingly, real-time PCR combined with multiplex pyrosequencing appears to be a reliable and easy-to-perform assay with high-throughput identification and fast TAT (~5 h).
ABSTRACT
We present a model-based parallel algorithm for origin and orientation refinement for 3D reconstruction in cryoTEM. The algorithm is based upon the Projection Theorem of the Fourier Transform. Rather than projecting the current 3D model and searching for the best match between an experimental view and the calculated projections, the algorithm computes the Discrete Fourier Transform (DFT) of each projection and searches for the central section ("cut") of the 3D DFT that best matches the DFT of the projection. Factors that affect the efficiency of a parallel program are first reviewed and then the performance and limitations of the proposed algorithm are discussed. The parallel program that implements this algorithm, called PO(2)R, has been used for the refinement of several virus structures, including those of the 500 Angstroms diameter dengue virus (to 9.5 Angstroms resolution), the 850 Angstroms mammalian reovirus (to better than 7A), and the 1800 Angstroms paramecium bursaria chlorella virus (to 15 Angstroms).
Subject(s)
Algorithms , Cryoelectron Microscopy/methods , Imaging, Three-Dimensional/methods , Microscopy, Electron, Transmission/methods , Viruses/ultrastructure , Dengue Virus/ultrastructure , Fourier Analysis , Models, Molecular , Orthoreovirus, Mammalian/ultrastructure , Phycodnaviridae/ultrastructureABSTRACT
The 3D reconstruction of virus structures at high resolution using CryoTEM data requires a very accurate rotational and translational alignment of individual views obtained experimentally. We discuss the geometrical foundations and the computational problems raised by rotational and translational alignment. We also outline the basic ideas for CTF correction.
Subject(s)
Computational Biology/methods , Image Processing, Computer-Assisted/methods , Imaging, Three-Dimensional/methods , Viruses/ultrastructure , Algorithms , Cryoelectron Microscopy , Electrons , Fourier Analysis , Microscopy, Electron/methods , Microscopy, Electron, Transmission , Models, Statistical , Viruses/chemistryABSTRACT
Reovirus is a useful model for addressing the molecular basis of membrane penetration by one of the larger nonenveloped animal viruses. We now report the structure of the reovirus virion at approximately 7.0 A resolution as obtained by electron cryomicroscopy and three-dimensional image reconstruction. Several features of the myristoylated outer capsid protein mu1, not seen in a previous X-ray crystal structure of the mu1-sigma3 heterohexamer, are evident in the virion. These features appear to be important for stabilizing the outer capsid, regulating the conformational changes in mu1 that accompany perforation of target membranes, and contributing directly to membrane penetration during cell entry.
Subject(s)
Capsid Proteins/chemistry , Capsid Proteins/ultrastructure , Cryoelectron Microscopy , Orthoreovirus/chemistry , Orthoreovirus/ultrastructure , Virion/ultrastructure , Algorithms , Amino Acid Sequence , Animals , Capsid Proteins/isolation & purification , Crystallography, X-Ray , Fourier Analysis , L Cells , Mice , Models, Chemical , Models, Molecular , Molecular Sequence Data , Myristic Acid/metabolism , Orthoreovirus/genetics , Protein Conformation , Protein Structure, Secondary , Sequence Homology, Amino Acid , Virion/growth & developmentABSTRACT
Three-dimensional reconstruction of large macromolecules like viruses at resolutions below 10 A requires a large set of projection images. Several automatic and semi-automatic particle detection algorithms have been developed along the years. Here we present a general technique designed to automatically identify the projection images of particles. The method is based on Markov random field modelling of the projected images and involves a pre-processing of electron micrographs followed by image segmentation and post-processing. The image is modelled as a coupling of two fields--a Markovian and a non-Markovian. The Markovian field represents the segmented image. The micrograph is the non-Markovian field. The image segmentation step involves an estimation of coupling parameters and the maximum á posteriori estimate of the realization of the Markovian field i.e, segmented image. Unlike most current methods, no bootstrapping with an initial selection of particles is required.
Subject(s)
Cryoelectron Microscopy/methods , Image Enhancement/methods , Image Processing, Computer-Assisted/methods , Markov Chains , Algorithms , Anisotropy , Bacteriophage T4/chemistry , Bacteriophage T4/ultrastructure , Imaging, Three-Dimensional , Pattern Recognition, Automated , Ross River virus/chemistry , Ross River virus/ultrastructure , Virion/chemistry , Virion/ultrastructureABSTRACT
Structural biology, in particular the structure determination of viruses and other large macromolecular complexes leads to data- and compute-intensive problems that require resources well beyond those available on a single system. Thus, there is an imperative need to develop parallel algorithms and programs for clusters and computational grids. We present one of the most challenging computational problems posed by the three-dimensional structure determination of viruses, the orientation refinement.
