Genetic and Environmental Risk for Chronic Pain and the Contribution of Risk Variants for Major Depressive Disorder: A Family-Based Mixed-Model Analysis

BackgroundChronic pain is highly prevalent and a significant source of disability, yet its genetic and environmental risk factors are poorly understood. Its relationship with major depressive disorder (MDD) is of particular importance. We sought to test the contribution of genetic factors and shared and unique environment to risk of chronic pain and its correlation with MDD in Generation Scotland: Scottish Family Health Study (GS:SFHS). We then sought to replicate any significant findings in the United Kingdom Biobank study.ConclusionsGenetic factors, as well as chronic pain in a partner or spouse, contribute substantially to the risk of chronic pain for an individual. Chronic pain is genetically correlated with MDD, has a polygenic architecture, and is associated with polygenic risk of MDD.     

Detection of MET Gene Copy Number in Cancer Samples Using the Droplet Digital PCR Method

Purpose

The analysis of MET gene copy number (CN) has been considered to be a potential biomarker to predict the response to MET-targeted therapies in various cancers. However, the current standard methods to determine MET CN are SNP 6.0 in the genomic DNA of cancer cell lines and fluorescence in situ hybridization (FISH) in tumor models, respectively, which are costly and require advanced technical skills and result in relatively subjective judgments. Therefore, we employed a novel method, droplet digital PCR (ddPCR), to determine the MET gene copy number with high accuracy and precision.

Methods

The genomic DNA of cancer cell lines or tumor models were tested and compared with the MET gene CN and MET/CEN-7 ratio determined by SNP 6.0 and FISH, respectively.

Results

In cell lines, the linear association of the MET CN detected by ddPCR and SNP 6.0 is strong (Pearson correlation = 0.867). In tumor models, the MET CN detected by ddPCR was significantly different between the MET gene amplification and non-amplification groups according to FISH (mean: 15.4 vs 2.1; P = 0.044). Given that MET gene amplification is defined as MET CN >5.5 by ddPCR, the concordance rate between ddPCR and FISH was 98.0%, and Cohen''s kappa coefficient was 0.760 (95% CI, 0.498–1.000; P <0.001).

Conclusions

The results demonstrated that the ddPCR method has the potential to quantify the MET gene copy number with high precision and accuracy as compared with the results from SNP 6.0 and FISH in cancer cell lines and tumor samples, respectively.     

Discovery of Metabolic Biomarkers for Duchenne Muscular Dystrophy within a Natural History Study

Serum metabolite profiling in Duchenne muscular dystrophy (DMD) may enable discovery of valuable molecular markers for disease progression and treatment response. Serum samples from 51 DMD patients from a natural history study and 22 age-matched healthy volunteers were profiled using liquid chromatography coupled to mass spectrometry (LC-MS) for discovery of novel circulating serum metabolites associated with DMD. Fourteen metabolites were found significantly altered (1% false discovery rate) in their levels between DMD patients and healthy controls while adjusting for age and study site and allowing for an interaction between disease status and age. Increased metabolites included arginine, creatine and unknown compounds at m/z of 357 and 312 while decreased metabolites included creatinine, androgen derivatives and other unknown yet to be identified compounds. Furthermore, the creatine to creatinine ratio is significantly associated with disease progression in DMD patients. This ratio sharply increased with age in DMD patients while it decreased with age in healthy controls. Overall, this study yielded promising metabolic signatures that could prove useful to monitor DMD disease progression and response to therapies in the future.     

Rice performance and natural infection with blast (Pyricularia oryzae Cav.) under different algalization techniques and rates of fertilizer nitrogen

Japonica rice, Giza 171, was inoculated with either a dry or fresh soil-based inoculum of cyanobacteria containingAnabaena cylindrica, Anabaena oryzae, Nostoc muscorum andTolypothrix tenuis together with fertilization with urea at 0, 36, 72, or 108 kg N/ha. Fresh inoculum enhanced plant growth, yield and N content in comparison with the dry one. The efficiency of nitrogen utilization from the urea at all N concentrations was improved by using the fresh inoculum. Natural infection with leaf and neck blast caused byPyricularia oryzae Cav. increased with increasing N fertilization. Algalization with the fresh inoculum decreased leaf blast while neck blast was slightly higher in the algalized sub-plots but without considerable yield damage.     

Inhibition of p38 MAPK facilitates ex vivo expansion of skin epithelial progenitor cells

Ex vivo expansion of skin epithelial stem cells has long attracted great interest because of the potential utilization in transplantation and gene therapy. The use of cultured stem or progenitor cells was limited by the lack of applicable culturing system with both satisfactory expansion efficacy and well suppressed differentiation ex vivo. The p38 mitogen-activated protein kinase (MAPK) pathways are responsible for cell growth and differentiation process. We investigated the function of p38 inhibitor SB203580 in the ex vivo expansion of skin epithelial progenitor cells by comparing media with or without addition of this inhibitor. Our results showed that the culturing medium with murine 3T3 feeder layers added with 10 μM SB203580 was more effective in promoting clonal growth of human skin epithelial progenitors or stem cells than the conventional medium without SB203580. The clone initial day in cells treated with 10 μM SB203580 came 2 d earlier with higher colony formation efficiency. The skin epithelial progenitor cells treated with 10 μM SB203580 formed clones that were uniformly smaller in size, longer in sustained proliferation, shorter in clone doubling time, higher in S-phase cells percentage, and lower in levels of differentiation markers such as K10 along with higher levels of stem-cell-associated markers such as p63, K15, and ABCG2 than those cultured in the conventional medium. Collectively, these results indicate that the p38 MAPK pathways inhibitor SB203580 can be used as a culture medium additive that helps to achieve more effective ex vivo expansion of skin epithelial progenitor cells.     

Enhancement of rice production using endophytic strains of Rhizobium leguminosarum bv. trifolii in extensive field inoculation trials within the Egypt Nile delta

This study assessed the ability of biofertilizer inoculants containing Rhizobium leguminosarum bv. trifolii to enhance production of rice (Oryza sativa L.) under actual agricultural conditions in the Nile delta. Large-scale field experiments evaluated 5 rice varieties inoculated with 7 endophytic rhizobial strains during 5 growing seasons, including at sites ranked as the world’s highest in rice production. Inoculation with single strains or multi-strain consortia significantly increased grain yield in 19 of the 24 trials. By combining superior rhizobial inoculants with agricultural extension training, grain yield increased up to 47% in farmers’ fields, with an average increase of 19.5%. Data on rice straw production, harvest index and the agronomic fertilizer N-use efficiency also indicated positive agronomic benefits of rhizobial inoculation. These results establish the merit of deploying our biofertilization strategy using selected rhizobial strains to promote rice production capacity while reducing the need for additional chemical N-fertilizer inputs to maintain agricultural sustainability and acceptable production economy. Technology transfer of this important translational research can significantly help to alleviate hunger and meet the nutritional needs of many people in developing countries.     

Water-soluble PDE4 inhibitors for the treatment of dry eye

PDE4 inhibitors have the potential to alleviate the symptoms and underlying inflammation associated with dry eye. Disclosed herein is the development of a novel series of water-soluble PDE4 inhibitors. Our studies led to the discovery of coumarin 18, which is effective in a rabbit model of dry eye and a tear secretion test in rats.