Three-dimensional visualization of forming Hepatitis C virus-like particles by electron-tomography

Association of Interleukin-27 rs 153109 Single Nucleotide Polymorphism with Spontaneous Resolution of Hepatitis C Virus - Genotype 4a Infection in Egyptian Patients

BACKGROUND

HCV is a major global health problem. IL-27 is a member of the IL-6/IL-12 cytokine family with a broad range of anti-inflammatory properties. Recent studies highlighted the effect of a SNP in the IL-27 promoter region on modulating the progression of infectious diseases and individual responses to therapy.

AIM OF THE WORK

The present study investigated the potential role of (-964 A/G) SNP in the promoter region of IL-27p28 gene (alleles rs153109) on the outcome of HCV infection among genotype 4a infected patients.

MATERIALS AND METHODS

HCV genotyping confirmed that all of the HCV-infected patients had genotype 4a infection. Genomic DNA was extracted from 111 patients with chronic HCV infection, 42 spontaneous resolvers (SR) and 16 healthy controls. IL- 27p28.rs153109 genotyping was assessed using PCR-RFLP then confirmed by DNA sequencing.

RESULTS

The frequency of IL-27-p28.rs153109AA, AG, and GG genotypes among chronically infected subjects were 74.8 %, 25.2%, and 0% while among the SR, they were 57.1%, 35.7%, and 7.14%, respectively. Our data show the unique presence of G/G genotype in the SR group (3 patients; 7.14%). Moreover, the "G" allele frequencies among chronic and resolved subjects were 12.6% and 25.0%, respectively (p=0.0136). Importantly, subjects with the GG genotype were more likely to clear their HCV infection than those with the AA genotype (p=0.0118).

CONCLUSIONS

HCV genotype 4a subjects with the IL-27-p28.rs153109 A/G and G/G genotype were more likely to clear their HCV infection. Therefore, we propose IL- 27p28.rs153109SNPas a genetic biomarker for predicting HCV infection outcome.

Combined approaches to study virus structures

A virus particle must work as a safe box for protecting its genome, but at the same time it has to undergo dramatic conformational changes in order to preserve itself by propagating in a cell infection. Thus, viruses are miniaturized wonders whose structural complexity requires them to be investigated by a combination of different techniques that can tackle both static and dynamic processes. In this chapter we will illustrate how major structural techniques such as X-ray crystallography and electron microscopy have been and can be combined with other techniques to determine the structure of complex viruses. The power of these hybrid method approaches are revealed through the various examples provided.

Evaluation of a multicore-optimized implementation for tomographic reconstruction

Tomography allows elucidation of the three-dimensional structure of an object from a set of projection images. In life sciences, electron microscope tomography is providing invaluable information about the cell structure at a resolution of a few nanometres. Here, large images are required to combine wide fields of view with high resolution requirements. The computational complexity of the algorithms along with the large image size then turns tomographic reconstruction into a computationally demanding problem. Traditionally, high-performance computing techniques have been applied to cope with such demands on supercomputers, distributed systems and computer clusters. In the last few years, the trend has turned towards graphics processing units (GPUs). Here we present a detailed description and a thorough evaluation of an alternative approach that relies on exploitation of the power available in modern multicore computers. The combination of single-core code optimization, vector processing, multithreading and efficient disk I/O operations succeeds in providing fast tomographic reconstructions on standard computers. The approach turns out to be competitive with the fastest GPU-based solutions thus far.