An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity

Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low‐coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high‐density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low‐density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.     

Nanocomposite scaffold seeded with mesenchymal stem cells for bone repair

The mechanical property of bone tissue scaffolds is one of the most important aspects in bone tissue engineering that has remained problematic. In our previous study, we fabricated a three‐dimensional scaffold from nano‐hydroxyapatite/gelatin (nHA/Gel) and investigated its efficiency in promoting bone regeneration both in vitro and in vivo. In the present study, the effect of adding silicon carbide (SiC) on the mechanical and biological behaviors of the nHA/Gel/SiC and bone regeneration in vivo were determined. nHA and SiC were synthesized and characterized by the X‐ray diffraction pattern and transmission electron microscope image. Layer solvent casting, freeze drying, and lamination techniques were applied to prepare these scaffolds. Then, the biocompatibility and cell adhesion behavior of the synthesized nHA/Gel/SiC scaffolds were investigated. For in vivo studies, rats were categorized into three groups: blank defect, blank scaffold, and rat bone marrow mesenchymal stem cells (rBM‐MSCs)/scaffold. After 1, 4, and 12 weeks post‐injury, the rats were sacrificed and the calvaria were harvested. Sections with a thickness of 5 µm thickness were prepared and stained with hematoxylin–eosin and Masson's Trichrome, and immunohistochemistry was performed. Our results showed that SiC effectively increased the mechanical properties of the nHA/Gel/SiC scaffold. No significant differences were observed in biocompatibility, cell adhesion, and cytotoxicity of the nHA/Gel/SiC in comparison with the nHA/Gel nanocomposite. Based on histological and immunohistochemical studies, both osteogenesis and collagenization were significantly higher in the rBM‐MSCs/scaffold group, quantitatively and qualitatively. The present study strongly suggests the potential of SiC as an alternative strategy to improve the mechanical and biological properties of bone tissue engineering scaffolds, and shows that the pre‐seeded nHA/Gel/SiC scaffold with rBM‐MSCs improves osteogenesis in the engineered bone implant.     

Relationship between myocardial bridge compression severity and haemodynamic perturbations

Objectives: This study aims to examine the alteration in coronary haemodynamics with increasing the severity of vessel compression caused by myocardial bridging (MB).

Methods: Angiography and intravascular ultrasound were performed in 10 patients with MB with varying severities of systolic compression in the left anterior descending (LAD) artery. Computer models of MB were developed and transient computational fluid dynamics simulations were performed to derive distribution of blood residence time and shear stress.

Results: With increasing the severity of bridge compression, a decreasing trend was observed in the shear stress over proximal segment whereas an increasing trend was found in the shear stress over bridge segment. When patients were divided into 2 groups based on the average systolic vessel compression in the whole cohort (%CR_ave = 27.38), patients with bridges with major systolic compression (>%CR_ave) had smaller shear stress and higher residence time in the proximal segment compared to those with bridges with minor systolic compression (<%CR_ave) (0.37?±?0.23 vs 0.69?±?0.29?Pa and 0.0037?±?0.0069 vs 0.022?±?0.0094?s). In contrast, patients with bridges with major systolic compression had greater shear stress in the bridge segment compared to those with bridges with minor systolic compression (2.49?±?2.06 vs 1.13?±?0.89?Pa). No significant difference was found in the distal shear stress of patients with bridges with major and minor systolic compression.

Conclusion: Our findings revealed a direct relationship between the severity of systolic compression of MB and haemodynamic perturbations in the proximal segment such that the increased systolic vessel compression was associated with decreased shear stress and increased blood residence time.     

Ischemia-reperfusion and immediate T cell responses

The pathogenesis of ischemia-reperfusion injury (IRI) is complex and not well understood. Inflammation plays an important role in IRI, with involvement of leukocytes, adhesion molecules, chemokines and cytokines. Emerging data suggest a role of T cells as mediators of IRI both in renal and extra-renal organs. Divergent roles of T cell subsets have also been elucidated, suggesting a more complicated role of T cells in the different phases of IRI. This review presents recent evidence from various animal models that advances our understanding of the role T cells play in IRI. These findings entertain the possibility of using immunotherapeutic agents for the prevention and treatment of IRI.     

Use of Coupled Al-Ag Bimetallic Cylindrical Nanoparticles to Improve the Photocurrent of a Thin-Film Silicon Solar Cell

In this paper, cylindrical shape coupled bimetallic plasmonic nanoparticles (NPs) were used to improve the performance of a thin-film silicon solar cell. Our design is based on the appropriate selection of the composition and morphology of the NPs to reach a cell with excellent optical properties. The specific interaction between the incident light and bimetallic NPs helps us to design better solar absorbers. Here, the FDTD method was used to evaluate the effect of cylindrical Al-Ag bimetallic NPs on the surface of a thin silicon absorber. At first, a unit cell with Al-Al paired nano-cylinders at the surface was evaluated and a photocurrent of 14.65 mA/cm² was obtained. In the case of a cell with paired Al-Ag bimetallic nano-cylinders, the photocurrent was increased to 16.15 mA/cm². This value was increased to 16.57 mA/cm² when paired polymetallic NPs were used. According to the results of this work, bimetallic and polymetallic nanoparticles can significantly improve the photocurrent of an ultra-thin silicon solar cell. The results of this work can be used to design better plasmonic-based light trapping systems for thin-film solar cells.

     

Evaluation of anticancer effects of cerium oxide nanoparticles on mouse fibrosarcoma cell line

Cerium oxide nanoparticles are associated with anticancer effects. While protecting normal cells, these nanoparticles exert their anticancer effects via oxidative stress and apoptosis in the cancer cells. In this study, the anticancer properties of nanoceria on fibrosarcoma cell line are evaluated. Cerium oxide nanoparticles were synthesized by the coprecipitation method and their anticancer effects on mouse fibrosarcoma tumor cells (WEHI164) were investigated. Viability assay was evaluated by MTT, and the DC-FDA assay performed for the detection of reactive oxygen species. For apoptosis assay, the annexin V/PI test was done as well as measuring the mRNA and protein expression levels of Bax and Bcl2 by real-time PCR and western blot method, respectively. Characterization of nanoceria reveals that synthesized nanoceria has cubic floruit structure with a size of about 30 nm. Toxicity assessment results show that nanoceria increases ROS levels and induced apoptosis in a dose-dependent manner in cancer cells (WEHI164), whereas low levels of toxicity were observed in normal cells (L929), even at the concentrations above 250 µg/ml in MTT assay. Real-time PCR and western blot assays showed that nanoceria could significantly increase the Bax expression in cancer cells. The results showed that nanoceria could act as a potential therapeutic agent for the treatment of fibrosarcoma.