Image Alignment for Tomography Reconstruction from Synchrotron X-Ray Microscopic Images

A synchrotron X-ray microscope is a powerful imaging apparatus for taking high-resolution and high-contrast X-ray images of nanoscale objects. A sufficient number of X-ray projection images from different angles is required for constructing 3D volume images of an object. Because a synchrotron light source is immobile, a rotational object holder is required for tomography. At a resolution of 10 nm per pixel, the vibration of the holder caused by rotating the object cannot be disregarded if tomographic images are to be reconstructed accurately. This paper presents a computer method to compensate for the vibration of the rotational holder by aligning neighboring X-ray images. This alignment process involves two steps. The first step is to match the “projected feature points” in the sequence of images. The matched projected feature points in the - plane should form a set of sine-shaped loci. The second step is to fit the loci to a set of sine waves to compute the parameters required for alignment. The experimental results show that the proposed method outperforms two previously proposed methods, Xradia and SPIDER. The developed software system can be downloaded from the URL, http://www.cs.nctu.edu.tw/~chengchc/SCTA or http://goo.gl/s4AMx.     

Identification and characterization of more than 4 million intervarietal SNPs across the group 7 chromosomes of bread wheat

Despite being a major international crop, our understanding of the wheat genome is relatively poor due to its large size and complexity. To gain a greater understanding of wheat genome diversity, we have identified single nucleotide polymorphisms between 16 Australian bread wheat varieties. Whole‐genome shotgun Illumina paired read sequence data were mapped to the draft assemblies of chromosomes 7A, 7B and 7D to identify more than 4 million intervarietal SNPs. SNP density varied between the three genomes, with much greater density observed on the A and B genomes than the D genome. This variation may be a result of substantial gene flow from the tetraploid Triticum turgidum, which possesses A and B genomes, during early co‐cultivation of tetraploid and hexaploid wheat. In addition, we examined SNP density variation along the chromosome syntenic builds and identified genes in low‐density regions which may have been selected during domestication and breeding. This study highlights the impact of evolution and breeding on the bread wheat genome and provides a substantial resource for trait association and crop improvement. All SNP data are publically available on a generic genome browser GBrowse at www.wheatgenome.info .     

Cell entry of bovine ephemeral fever virus requires activation of Src‐JNK‐AP1 and PI3K‐Akt‐NF‐κB pathways as well as Cox‐2‐mediated PGE2/EP receptor signalling to enhance clathrin‐mediated virus endocytosis

Although we have previously demonstrated that cell entry of bovine ephemeral fever virus (BEFV) follows a clathrin‐mediated and dynamin 2‐dependent endocytosis pathway, the cellular mechanism mediating virus entry remains unknown. Here, we report that BEFV triggers simultaneously Src‐JNK‐AP1 and PI3K‐Akt‐NF‐κB signalling pathways in the stage of virus binding to induce clathrin and dynamin 2 expressions, while vesicular stomatitis virus only activates Src‐JNK signalling to enhance its entry. Activation of these pathways by ultraviolet‐inactivated BEFV suggests a role for virus binding but not viral internalization and gene expression. By blocking these signalling pathways with specific inhibitors, BEFV‐induced expressions of clathrin and dynamin 2 were significantly diminished. By labelling BEFV with 3,3′‐dilinoleyloxacarbocyanine perchlorate to track viral entry, we found that virus entry was hindered by both Src and Akt inhibitors, suggesting that these signalling pathways are crucial for efficient virus entry. In addition, BEFV also triggers Cox‐2‐catalysed prostaglandin E₂ (PGE₂) synthesis and induces expressions of G‐protein‐coupled E‐prostanoid (EP) receptors 2 and 4, leading to amplify signal cascades of Src‐JNK‐AP1 and PI3K‐Akt‐NF‐κB, which elevates both clathrin and dynamin 2 expressions. Furthermore, pretreatment of cells with adenylate cyclase (cAMP) inhibitor SQ22536 reduced BEFV‐induced Src phosphorylation as well as clathrin and dynamin 2 expressions. Our findings reveal for the first time that BEFV activates the Cox‐2‐mediated PGE₂/EP receptor signalling pathways, further enhancing Src‐JNK‐AP1 in a cAMP‐dependent manner and PI3K‐Akt‐NF‐κB in a cAMP‐independent manner. Accordingly, BEFV stimulates PGE₂/EP receptor signalling amplifying Src‐JNK‐AP1 and PI3K‐Akt‐NF‐κB pathways in an autocrine or paracrine fashion to enhance virus entry.     

The complete methylome of Helicobacter pylori UM032

Background

The genome of the human gastric pathogen Helicobacter pylori encodes a large number of DNA methyltransferases (MTases), some of which are shared among many strains, and others of which are unique to a given strain. The MTases have potential roles in the survival of the bacterium. In this study, we sequenced a Malaysian H. pylori clinical strain, designated UM032, by using a combination of PacBio Single Molecule, Real-Time (SMRT) and Illumina MiSeq next generation sequencing platforms, and used the SMRT data to characterize the set of methylated bases (the methylome).

Results

The N4-methylcytosine and N6-methyladenine modifications detected at single-base resolution using SMRT technology revealed 17 methylated sequence motifs corresponding to one Type I and 16 Type II restriction-modification (R-M) systems. Previously unassigned methylation motifs were now assigned to their respective MTases-coding genes. Furthermore, one gene that appears to be inactive in the H. pylori UM032 genome during normal growth was characterized by cloning.

Conclusion

Consistent with previously-studied H. pylori strains, we show that strain UM032 contains a relatively large number of R-M systems, including some MTase activities with novel specificities. Additional studies are underway to further elucidating the biological significance of the R-M systems in the physiology and pathogenesis of H. pylori.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1585-2) contains supplementary material, which is available to authorized users.     

A Study on the Impact of Hydroxypropyl Methylcellulose on the Viscosity of PEG Melt Suspensions Using Surface Plots and Principal Component Analysis

An understanding of the rheological behaviour of polymer melt suspensions is crucial in pharmaceutical manufacturing, especially when processed by spray congealing or melt extruding. However, a detailed comparison of the viscosities at each and every temperature and concentration between the various grades of adjuvants in the formulation will be tedious and time-consuming. Therefore, the statistical method, principal component analysis (PCA), was explored in this study. The composite formulations comprising polyethylene glycol (PEG) 3350 and hydroxypropyl methylcellulose (HPMC) of ten different grades (K100 LV, K4M, K15M, K100M, E15 LV, E50 LV, E4M, F50 LV, F4M and Methocel VLV) at various concentrations were prepared and their viscosities at different temperatures determined. Surface plots showed that concentration of HPMC had a greater effect on the viscosity compared to temperature. Particle size and size distribution of HPMC played an important role in the viscosity of melt suspensions. Smaller particles led to a greater viscosity than larger particles. PCA was used to evaluate formulations of different viscosities. The complex viscosity profiles of the various formulations containing HPMC were successfully classified into three clusters of low, moderate and high viscosity. Formulations within each group showed similar viscosities despite differences in grade or concentration of HPMC. Formulations in the low viscosity cluster were found to be sprayable. PCA was able to differentiate the complex viscosity profiles of different formulations containing HPMC in an efficient and time-saving manner and provided an excellent visualisation of the data.KEY WORDS: hydroxypropyl methylcellulose, polymers, principal component analysis, surface plot, viscosity     

Impact of Bisphosphonate-related Osteonecrosis of the Jaw on Osteoporotic Patients after Dental Extraction: A Population-Based Cohort Study

Background and Aims

Little is currently known about the risk of developing bisphosphonate-related osteonecrosis of the jaw (BRONJ). This study sought to determine the incidence of BRONJ in osteoporotic patients. We also sought to identify the nature and types of risk factors of osteonecrosis of jaw (ONJ) related to the use of oral bisphosphonates (BPs).

Materials and Methods

Data from the National Health Insurance system of Taiwan. This cohort study included 19,399 adult osteoporosis patients received dental extraction in 2000-2010 (osteoporosis cohort) and 38,669 age and gender matched comparisons selected from dental extraction people without osteoporosis and osteonecrosis history (comparison cohort). All study subjects were followed from the date of their dental extraction (index date) to the development of ONJ and were included in the study up to 2011 or were lost to the study, whichever occurred first. Cox proportional hazard regression was used to estimate the hazard ratio and 95% confidence intervals for the two cohorts.

Results

Patients with osteoporosis had a significantly higher risk to develop ONJ than healthy persons (adjusted HR, 2.05; 95% confidence interval, 1.58–2.65). The risk of ONJ increased with the severity of osteoporosis, no matter whether patient with cancer or not. A cumulative effect of dental extraction frequency may increase the risk of ONJ.

Conclusions

We concluded that ONJ is caused by a number of factors. Osteoporosis and past dental history play the very important roles, while BPs play the synergistic effect.     

The first description of population density and habitat use of the mainland clouded leopard Neofelis nebulosa within a logged-primary forest in South East Asia

The mainland clouded leopard (Neofelis nebulosa) is classified as vulnerable under the IUCN Red List, meaning that it faces a high risk of extinction in the wild. However, hardly any ecological research has been published on this species apart from several radiotelemetry studies in Thailand and Nepal, and one camera-trapping study in India. Here we present findings on the clouded leopard from a camera-trapping study conducted in Temengor forest reserve (a logged-over forest) and Royal Belum State Park (a primary forest) within Peninsular Malaysia. Using the spatially-explicit capture-recapture method, the density from Temengor forest reserve and Royal Belum State Park was estimated at 3.46 ± SE 1.00 and 1.83 ± SE 0.61, respectively. Clouded leopard habitat use was found to be highly influenced by the availability of small and medium prey species and therefore intrinsically highlights the potential conservation importance of species such as pig-tailed macaques, porcupine, mouse deer and small carnivores. These findings provide the first estimates of density and habitat use of this species in a logged-primary forest from both Peninsular Malaysia and South East Asia. Our study provides important baseline information on clouded leopards and contributes to filling up the knowledge gap that exists in understanding the population ecology of this species, not only within Peninsular Malaysia, but also on a regional level.     

Increased Susceptibility of Humanized NSG Mice to Panton-Valentine Leukocidin and Staphylococcus aureus Skin Infection

Staphylococcus aureus is a leading cause of skin and soft-tissue infections worldwide. Mice are the most commonly used animals for modeling human staphylococcal infections. However a supra-physiologic S. aureus inoculum is required to establish gross murine skin pathology. Moreover, many staphylococcal factors, including Panton-Valentine leukocidin (PVL) elaborated by community-associated methicillin-resistant S. aureus (CA-MRSA), exhibit selective human tropism and cannot be adequately studied in mice. To overcome these deficiencies, we investigated S. aureus infection in non-obese diabetic (NOD)/severe combined immune deficiency (SCID)/IL2rγ^null (NSG) mice engrafted with human CD34⁺ umbilical cord blood cells. These “humanized” NSG mice require one to two log lower inoculum to induce consistent skin lesions compared with control mice, and exhibit larger cutaneous lesions upon infection with PVL⁺ versus isogenic PVL^- S. aureus. Neutrophils appear important for PVL pathology as adoptive transfer of human neutrophils alone to NSG mice was sufficient to induce dermonecrosis following challenge with PVL⁺ S. aureus but not PVL^- S. aureus. PMX53, a human C5aR inhibitor, blocked PVL-induced cellular cytotoxicity in vitro and reduced the size difference of lesions induced by the PVL⁺ and PVL^- S. aureus, but PMX53 also reduced recruitment of neutrophils and exacerbated the infection. Overall, our findings establish humanized mice as an important translational tool for the study of S. aureus infection and provide strong evidence that PVL is a human virulence factor.