抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

J. Appl. Cryst.の発刊に際して

Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.

/pdf/macromolecular-structure-determination-using-x-rays-neutrons-7udc75ny0s.pdf

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

Interpretation of X-ray Powder Diffraction Patterns . By H. Lipson and H. Steeple. Pp. viii + 335 + 3 plates. (Mac-millan: London; St Martins Press: New York, May 1970.) £4.

X-Ray Diffraction

Recent advances in nanoscience and nanotechnology radically changed the way we diagnose, treat, and prevent various diseases in all aspects of human life. Silver nanoparticles (AgNPs) are one of the most vital and fascinating nanomaterials among several metallic nanoparticles that are involved in biomedical applications. AgNPs play an important role in nanoscience and nanotechnology, particularly in nanomedicine. Although several noble metals have been used for various purposes, AgNPs have been focused on potential applications in cancer diagnosis and therapy. In this review, we discuss the synthesis of AgNPs using physical, chemical, and biological methods. We also discuss the properties of AgNPs and methods for their characterization. More importantly, we extensively discuss the multifunctional bio-applications of AgNPs; for example, as antibacterial, antifungal, antiviral, anti-inflammatory, anti-angiogenic, and anti-cancer agents, and the mechanism of the anti-cancer activity of AgNPs. In addition, we discuss therapeutic approaches and challenges for cancer therapy using AgNPs. Finally, we conclude by discussing the future perspective of AgNPs.

/pdf/silver-nanoparticles-synthesis-characterization-properties-1gs52z8tm7.pdf

Silver Nanoparticles: Synthesis, Characterization, Properties, Applications, and Therapeutic Approaches

Recovering a signal from its Fourier magnitude is referred to as phase retrieval, which occurs in different fields of engineering and applied physics. This paper gives a new characterization of the phase retrieval problem. Particularly useful is the analysis revealing that the common gradient-based regularization does not restrict the set of solutions to a smaller set. Specifically focusing on binary signals, we show that a box relaxation is equivalent to the binary constraint for Fourier-types of phase retrieval. We further prove that binary signals can be recovered uniquely up to trivial ambiguities under certain conditions. Finally, we use the characterization theorem to develop an efficient denoising algorithm.

One-Dimensional Phase Retrieval: Regularization, Box Relaxation and Uniqueness

Data Efficient X-ray Phase Tomography with Self-calibrated Sandpaper Analyzer

When x-rays penetrate soft matter, their phase changes more rapidly than their amplitude. In- terference effects visible with high brightness sources creates higher contrast, edge enhanced images. When the object is piecewise smooth (made of big blocks of a few components), such higher con- trast datasets have a sparse solution. We apply basis pursuit solvers to improve SNR, remove ring artifacts, reduce the number of views and radiation dose from phase contrast datasets collected at the Hard X-Ray Micro Tomography Beamline at the Advanced Light Source. We report a GPU code for the most computationally intensive task, the gridding and inverse gridding algorithm (non uniform sampled Fourier transform).

Compressive Phase Contrast Tomography

Our goal was to prepare an X-ray Fluorescence Holography (XFH) experiment at ESRF, in which the holographic information is approximately 0.3% of the overall isotropic fluorescent radiation. This requires a very pure fluorescent signal and the highest possible count rate. Therefore, we designed a focusing analyzer system with large solid angle acceptance. It consists of a sagittally bent pyrolithic graphite crystals with large solid angle acceptance used in the parafocusing mode for the meridional plane. We successfully applied it to collect a large fraction of isotropically emitted Fe, Ni and Pd K (alpha ) fluorescent photons with the [002] and [006] graphite reflections, respectively. After characterizing the phase space efficiency (angular acceptance, focal spot shape) of a 200 mm long, doubly focusing analyzer, we developed a full circular one (220 mm diameter) to increase the solid angle acceptance to approximately 2 10 -2 sr, in view of an XFH experiment on MBE grown thin films. This analyzer can be used more generally at K and L edges for atoms with Z greater than or equal to 20.

Doubly focusing crystal analyzer for x-ray fluorescence holography

The latest development of ultrafast free electron laser makes it now possible to perform single molecule diffraction
imaging. In such an experiment, two-dimensional (2D) diffraction images of randomly oriented molecules of the
same type (single molecules) can be captured within femtosecond exposure time. These images can then be
used to deduce the 3D structure of the molecule. Two of the most challenging problems that must be solved in
order to obtain a high resolution 3D reconstruction are: 1) the determination of the relative orientations of 2D
diffraction images; 2) the retrieval of the phase information of a reconstructed 3D diffraction pattern. In this
paper, we will focus on the first problem and discuss the use of common curve detection techniques to deduce
the relative orientations of 2D diffraction images produced from single-molecule diffraction experiments. Such a
technique is based on the fact that Ewald spheres associated with two diffraction images of the same molecule
intersect along a common curve in the reciprocal space. By detecting these curves on each diffraction image, we
can deduce the relative orientations of diffraction images by solving an eigenvalue problem. When the radius of
the Ewald sphere is sufficiently large relatively to the region of reciprocal space we are interested in, the Ewald
sphere becomes flat near the origin of the reciprocal space, and common curves reduce to common lines. In
this case, the orientation determination problem is similar to the one that arises in single particle cryo-electron
microscopy. The recent work of Singer and Shkolnisky [1] shows that the orientation determination problem
can be solved by computing the largest eigenvalues of a symmetric matrix constructed from the common lines
identified among cryo-EM projection images. In this paper, we will extend their technique to diffraction images
on which common curves can be identified.

Stefano Marchesini

Papers

One-Dimensional Phase Retrieval: Regularization, Box Relaxation and Uniqueness

Data Efficient X-ray Phase Tomography with Self-calibrated Sandpaper Analyzer

Compressive Phase Contrast Tomography

Doubly focusing crystal analyzer for x-ray fluorescence holography

Orientation determination for 3D single molecule diffraction imaging