Enhancing the DNA yield intended for microbial sequencing from a low-biomass chlorinated drinking water.

DNA extraction yield from drinking water distribution systems and premise plumbing is a key metric for any downstream analysis such as 16S amplicon or metagenomics sequencing. This research aimed to optimize DNA yield from low-biomass (chlorinated) reverse osmosis-produced tap water by evaluating the impact of different factors during the DNA extraction procedure. The factors examined are (1) the impact of membrane materials and their pore sizes; (2) the impact of different cell densities; and (3) an alternative method for enhancing DNA yield via incubation (no nutrient spiking). DNA from a one-liter sampling volume of RO tap water with varying bacterial cell densities was extracted with five different filter membranes (mixed ester cellulose 0.2 µm, polycarbonate 0.2 µm, polyethersulfone 0.2 and 0.1 µm, polyvinylidene fluoride 0.1 µm) for biomass filtration. Our results show that (i) smaller membrane pore size solely did not increase the DNA yield of low-biomass RO tap water; (ii) the DNA yield was proportional to the cell density and substantially dependent on the filter membrane properties (i.e., the membrane materials and their pore sizes); (iii) by using our optimized DNA extraction protocol, we found that polycarbonate filter membrane with 0.2 µm pore size markedly outperformed in terms of quantity (DNA yield) and quality (background level of 16S gene copy number) of recovered microbial DNA; and finally, (iv) for one-liter sampling volume, incubation strategy enhanced the DNA yield and enabled accurate identification of the core members (i.e., Porphyrobacter and Blastomonas as the most abundant indicator taxa) of the bacterial community in low-biomass RO tap water. Importantly, incorporating multiple controls is crucial to distinguish between contaminant/artefactual and true taxa in amplicon sequencing studies of low-biomass RO tap water.

Evaluation of DNA extraction yield from a chlorinated drinking water distribution system.

Desalination technology based on Reverse Osmosis (RO) membrane filtration has been resorted to provide high-quality drinking water. RO produced drinking water is characterized by a low bacterial cell concentration. Monitoring microbial quality and ensuring membrane-treated water safety has taken advantage of the rapid development of DNA-based techniques. However, the DNA extraction process from RO-based drinking water samples needs to be evaluated regarding the biomass amount (filtration volume) and residual disinfectant such as chlorine, as it can affect the DNA yield. We assessed the DNA recovery applied in drinking water microbiome studies as a function of (i) different filtration volumes, (ii) presence and absence of residual chlorine, and (iii) the addition of a known Escherichia coli concentration into the (sterile and non-sterile, chlorinated and dechlorinated) tap water prior filtration, and directly onto the (0.2 µm pore size, 47 mm diameter) mixed ester cellulose membrane filters without and after tap water filtration. Our findings demonstrated that the co-occurrence of residual chlorine and low biomass/cell density water samples (RO-treated water with a total cell concentration ranging between 2.47 × 102-1.5 × 103 cells/mL) failed to provide sufficient DNA quantity (below the threshold concentration required for sequencing-based procedures) irrespective of filtration volumes used (4, 20, 40, 60 L) and even after performing dechlorination. After exposure to tap water containing residual chlorine (0.2 mg/L), we observed a significant reduction of E. coli cell concentration and the degradation of its DNA (DNA yield was below detection limit) at a lower disinfectant level compared to what was previously reported, indicating that free-living bacteria and their DNA present in the drinking water are subject to the same conditions. The membrane spiking experiment confirmed no significant impact from any potential inhibitors (e.g. organic/inorganic components) present in the drinking water matrix on DNA extraction yield. We found that very low DNA content is likely to be the norm in chlorinated drinking water that gives hindsight to its limitation in providing robust results for any downstream molecular analyses for microbiome surveys. We advise that measurement of DNA yield is a necessary first step in chlorinated drinking water distribution systems (DWDSs) before conducting any downstream omics analyses such as amplicon sequencing to avoid inaccurate interpretations of results based on very low DNA content. This study expands a substantial source of bias in using DNA-based methods for low biomass samples typical in chlorinated DWDSs. Suggestions are provided for DNA-based research in drinking water with residual disinfectant.

Antagonistic selection between adult thorax and wing size in field released Drosophila melanogaster independent of thermal conditions.

Attempts to explain size variation in Drosophila and other small insects often focus on the larval stage and association between development time and size, but patterns are also influenced by direct selection on size-related traits in the adults. Here we use multiple field releases of Drosophila melanogaster to test the association between size and one component of field fitness, the ability of Drosophila to locate resources for feeding and breeding. We find antagonistic selection between wing length and thorax length in both males and females, such that capture at baits is higher for flies with relatively larger thorax lengths and smaller wings. However flies with large wings relative to thoraces disperse further as reflected in the longer distances moved to baits. These patterns did not depend strongly on weather conditions, suggesting that selection on adult size is at least partly independent of temperature. Antagonistic selection between size traits can generate changes in size along gradients if the distribution of resources in the environment varies and selects for different dispersal patterns, particularly as dispersal is relatively higher under warmer conditions.

Whole-body bioluminescent imaging of human uveal melanoma in a new mouse model of local tumor growth and metastasis.

PURPOSE: Human uveal melanoma develops in one of the most capillary-rich tissues of the body and has a pure hematogenous dissemination. Radiodiagnostic examinations, such as ultrasonic diagnostic resonance imaging and chest radiographs plus liver enzyme studies in blood, are methods used to detect liver and other distant metastases in patients. Nevertheless, the mortality rate is high, because of the frequent occurrence of metastases and the lack of systemic therapy. Therefore, the development of novel anticancer strategies is urgent, and more sensitive and less invasive methods of detecting and monitoring in vivo tumor growth and metastatic disease in cancer models are needed. METHODS: A luciferase (Luc)-positive human uveal melanoma cell line (OCM-1 FRT/luc) was established. Tumor cells were inoculated into the anterior chamber of murine eyes for induction of orthotopic growth or into the left heart ventricle to mimic hematogenous micrometastatic spread. Development of metastases and tumor growth was monitored weekly by whole-body bioluminescent reporter imaging (BLI). RESULTS: Injection of cancer cells into the anterior chamber of the eye of mice closely mimicked orthotopic tumor growth of uveal melanoma. Tumor progression could be quantitatively monitored 3 weeks after inoculation of 10(5) OCM-1 FRT/luc cells. Of the mice injected, 83% exhibited a detectable tumor within 5 weeks. Intracardiac injection of tumor cells resulted in metastatic growth, especially in bone. Mice had bone (maxillofacial region and femora) and visceral (lung and mediastinum) metastases after 4 to 6 weeks. OCM-1 FRT/luc cells may also have a propensity to colonize the eye after intracardiac inoculation. CONCLUSIONS: BLI enables continuous quantitative monitoring in the same animal of growth kinetics for each tumor and its metastases. This model will accelerate the understanding of the pathogenesis and treatment of uveal melanoma and metastasis.