The SARS-Unique Domain (SUD) of SARS Coronavirus Contains Two Macrodomains That Bind G-Quadruplexes

Since the outbreak of severe acute respiratory syndrome (SARS) in 2003, the three-dimensional structures of several of the replicase/transcriptase components of SARS coronavirus (SARS-CoV), the non-structural proteins (Nsps), have been determined. However, within the large Nsp3 (1922 amino-acid residues), the structure and function of the so-called SARS-unique domain (SUD) have remained elusive. SUD occurs only in SARS-CoV and the highly related viruses found in certain bats, but is absent from all other coronaviruses. Therefore, it has been speculated that it may be involved in the extreme pathogenicity of SARS-CoV, compared to other coronaviruses, most of which cause only mild infections in humans. In order to help elucidate the function of the SUD, we have determined crystal structures of fragment 389–652 (“SUDcore”) of Nsp3, which comprises 264 of the 338 residues of the domain. Both the monoclinic and triclinic crystal forms (2.2 and 2.8 Å resolution, respectively) revealed that SUDcore forms a homodimer. Each monomer consists of two subdomains, SUD-N and SUD-M, with a macrodomain fold similar to the SARS-CoV X-domain. However, in contrast to the latter, SUD fails to bind ADP-ribose, as determined by zone-interference gel electrophoresis. Instead, the entire SUDcore as well as its individual subdomains interact with oligonucleotides known to form G-quadruplexes. This includes oligodeoxy- as well as oligoribonucleotides. Mutations of selected lysine residues on the surface of the SUD-N subdomain lead to reduction of G-quadruplex binding, whereas mutations in the SUD-M subdomain abolish it. As there is no evidence for Nsp3 entering the nucleus of the host cell, the SARS-CoV genomic RNA or host-cell mRNA containing long G-stretches may be targets of SUD. The SARS-CoV genome is devoid of G-stretches longer than 5–6 nucleotides, but more extended G-stretches are found in the 3′-nontranslated regions of mRNAs coding for certain host-cell proteins involved in apoptosis or signal transduction, and have been shown to bind to SUD in vitro. Therefore, SUD may be involved in controlling the host cell's response to the viral infection. Possible interference with poly(ADP-ribose) polymerase-like domains is also discussed

Retinal fundus image constrast normalization using mixture of gaussians

We present a fast and robust method to correct contrast variation in retinal fundus imagery. The technique uses a mixture of Gaussians to model the bias of the intensity variation. Typically a three or four component mixture is sufficient to characterize the principal variation due to the spherical geometry of the retina, the high-contrast reflection off the optic nerve and the darker macula. We compare the results with a non-parametric, filtering approach on a standard diabetic retinopathy database of 89 images. Our results indicate that a parametric approach using mixture Gaussian is better at contrast stretching in lesion regions making is an effective pre-processing step for manual and computer aided diagnostic techniques

Robust detection of microaneurysms for sight threatening retinopathy screening

Diabetic retinopathy is one of the major causes of blindness. However diabetic retinopathy does not usually cause a loss of sight until it has reached an advanced stage. The earliest sign of the disease are microaneurysms (MA) which appear as small red dots on retinal fundus images. Various screening programmes have been established in the UK and other countries to collect and assess images on a regular basis, especially in the diabetic population. A considerable amount of time and money is spent in manually grading these images, a large percentage of which are normal. By automatically identifying the normal images, the manual workload and costs could be reduced greatly while increasing the effectiveness of the screening programmes. A novel method of microaneurysm detection from digital retinal screening images is proposed. It is based on filtering using complex-valued circular-symmetric filters, and an eigen-image, morphological analysis of the candidate regions to reduce the false-positive rate. We detail the image processing algorithms and present results on a typical set of 89 image from a published database. Our method is shown to have a best operating sensitivity of 82.6% at a specificity of 80.2% which makes it viable for screening. We discuss the results in the context of a model of visual search and the ROC curves that it can predict

One-Step Fabrication of Amino-Functionalized Fe₃O₄@SiO₂ Core-Shell Magnetic Nanoparticles as a Potential Novel Platform for Removal of Cadmium (II) from Aqueous Solution

Fe3O4@SiO2-NH2 core-shell magnetic nanoparticles were developed by a rapid one-step precipitation route followed by reverse microemulsion and amine functionalization. In this study, an Fe3O4@SiO2-NH2 nanoparticle was used to evaluate its adsorption efficiency for the treatment of a synthetic solution of Cd(II) ion. The structural and physicochemical properties of Fe3O4@SiO2-NH2 nanoparticles were characterized by XRD, SEM-EDAX, TEM, FTIR and TGA. From the TEM analysis, the morphology of Fe3O4@SiO2-NH2 was found as 100–300 nm. In TGA, the first weight loss was noticed between 373 and 573 K, the second was between 673 and 773 K and the final weight loss took place above 773 K. Batch experimental tests, such as pH, dosage of Fe3O4@SiO2-NH2, Cd(II) ion concentration, temperature as well as interaction time, were conducted and evaluated. Experimental study data were used for the non-linear forms exhibited by isotherms and kinetics of the sorption procedure. The equilibrium adsorption observations were adequately combined with pseudo-first-order kinetics as well as Freundlich isotherm. Monolayer maximum adsorption capacity was found to be 40.02 mg/g, recorded at pH 6 with an interaction time of 30 min, temperature of 303 K and sorbent dose of 2.0 g/L. The thermodynamic study indicated that the adsorption process was an exothermic, spontaneous reaction (−∆oo = −15.46–7.81 (kJ/mol)). The as-synthesized sorbent had excellent recyclability, and its adsorption efficiency was maintained after five cycles of reuse. The findings of the study exhibited the magnetic Fe3O4@SiO2-NH2-nanoparticle as an alternative effective adsorbent in eradicating Cd(II) ions from aqueous solution