Impact of purified water quality on molecular biology experiments

Effects of reverse osmosis membrane replacement of pure water system on clinical chemistry and immunoassay in clinical laboratory

Introduction

Reverse osmosis (RO) membrane, key component of water-purifying equipment, is often stored in protection fluid containing substances such as glycerol, which may contaminate the water at replacement. This study aims to explore the effects of RO membrane replacement on clinical chemistry and immunoassay, particularly triglyceride (TG), providing reference for managing test interference caused by RO membrane replacement.

Materials and methods

The RO membrane of water-purifying equipment A, which provided water to C16000 biochemistry analyzer (Abbott Laboratories, Abbott Park, USA) and E801 electrochemiluminescence analyzer (Roche, Basel, Switzerland), was replaced. Water resistivity was recorded, and quality control (QC) tests were performed on C16000 and E801. Moreover, TG was measured in 29 of selected serum samples on C16000 at 0.5h and 10.5h after RO membrane replacement and on reference biochemistry analyzer BS2000M (Mindray Biomedical Electronics Co., Shenzhen, China), which was connected to water-purifying equipment B without RO membrane replacement. Finally, blank, calibrator 1 and calibrator 2 of TG reagent were measured on C16000 before and at 0.5h, 2.5h and 10.5h after RO membrane replacement. All statistical analyses of data were done using GraphPad Prism (GraphPad Software Inc., San Diego, USA), and a value of P < 0.05 was considered statistically significant.

Results

After RO membrane replacement, all QC results of clinical chemistry and immune tests passed except TG that showed positive bias of 536% and 371% at two levels, respectively. Moreover, TG results of the same serum samples were significantly higher at 0.5h than 10.5h after RO membrane replacement. Meanwhile, there was worse agreement and correlation of TG results between C16000 and BS2000M at 0.5h than 10.5h after replacement. Furthermore, the absorbance of TG blank, calibrator 1 and calibrator 2 was significantly higher at 0.5h and 2.5h after replacement than before replacement, and the absorbance gradually returned to normal value at 10.5h after replacement.

Conclusions

Replacement of RO membrane could cause significant interference to TG test while have no effects on other laboratory tests performed in the study, which may be due to glycerol contamination. Our data provides important reference for management of test interference caused by RO membrane replacement. Clinical laboratory should observe the effects of RO membrane replacement on laboratory tests through both water quality monitoring and QC detection.

Improvement in cyst recovery and molecular detection of Giardia duodenalis from stool samples

Molecular detection of Giardia duodenalis by polymerase chain reaction (PCR) is difficult in faecal samples due to inhibitors that contaminate DNA preparations, or due to low cyst concentrations. In order to eliminate inhibitors, improve cyst recovery and molecular detection of G. duodenalis, different types of water, distillates (MDs), deionized (MDz), injection (MI) or Milli-Q^® (MM) were used instead of formaldehyde (F) in the laboratory routine method (Ritchie). Cysts were isolated from faecal samples with low cyst concentrations (< 1 cyst/field), medium (1-2 cysts/field) or high (> 2 cysts/field). Cyst recovery was improved using all water types (MDs, MDz, MI, MM) compared to formaldehyde. At all cyst concentrations, the use of MM consistently showed the greatest recovery of G. duodenalis cysts . DNA samples from recovered cysts were tested for the glutamate dehydrogenase (GDH) and β-giardin (βg) genes. The use of Milli-Q^® water allowed to detect both genes in all cyst concentrations, including low. The method processed with the other types of water amplified these genes at high and medium cyst concentrations. GDH and βg genes were not detected when the sample was processed with formaldehyde. These experimental results were confirmed in clinical samples. The results suggest that Milli-Q^® water provides the highest cyst recovery from stool samples and, correspondingly, the highest sensitivity for detecting G. duodenalis by microscopy or PCR for GDH and βg genes, even at low concentration of cysts.

Producing standard damaged DNA samples by heating: pitfalls and suggestions

Heat-mediated hydrolysis of DNA is a simple and inexpensive method for producing damaged samples in vitro. Despite heat-mediated DNA hydrolysis is being widely used in forensic and clinical validation procedures, the lack of standardized procedures makes it impossible to compare the intra and inter-laboratory outcomes of the damaging treatments. In this work, a systematic approach to heat induced DNA hydrolysis was performed at 70 °C for 0-18 h to test the role both of the hydrolysis buffer and of the experimental conditions. Specifically, a trial DNA sample, resuspended in three different media (ultrapure water, 0.1% DEPC-water and, respectively, TE) was treated both in Eppendorf tubes ("Protocol P") and in Eppendorf tubes provided with screwcaps ("Protocol S"). The results of these comparative tests were assessed by normalization of the qPCR results. DEPC-water increased the degradation of the samples up to about 100 times when compared to the ultrapure water. Conversely, the TE protected the DNA from degradation whose level was about 1700 times lower than in samples treated in ultrapure water. Even the employment of the "Protocol S" affected the level of degradation, by consistently increasing it (up to about 180 times in DEPC-water). Thus, this comparative approach showed that even seemingly apparently trivial and often underestimated parameters modify the degradation level up to 2-3 orders of magnitude. The chemical-physical reasons of these findings are discussed together with the role of potential factors such as enhanced reactivity of CO₂, ROS, NO_x and pressure, which are likely to be involved. Since the intra and inter-laboratory comparison of the outcomes of the hydrolytic procedure is the first step toward its standardization, the normalization of the qPCR data by the UV/qPCR ratio seems to be the simplest and most reliable way to allow this. Finally, the supplying (provided with the commercial qPCR kits) of a DNA sample whose degree of degradation is well documented could be helpful in ISO/IEC 17025 validation procedures and in proficiency testing.

Review of the impact of water quality on reliable laboratory testing and correlation with purification techniques

In recent years, many rapid and automated instruments with highly complex testing methodologies have been introduced to our laboratories, almost all of which require the use of water. Many investigators have discussed the impact of water quality on the accuracy and reliability of clinical laboratory testing and technologies. Evaluation of water quality and specifications according to international standards and guidelines has helped laboratories to judge water quality before using the water in question as part of testing. In the past few years, dramatic introduction of different water purification technologies has shown significant improvements in laboratory testing accuracy. In this review, we delve into the intricate factors that influence water quality.

Manufacture of β-TCP/alginate scaffolds through a Fab@home model for application in bone tissue engineering

The growing need to treat bone-related diseases in an elderly population compels the development of novel bone substitutes to improve patient quality of life. In this context, the advent of affordable and effective rapid prototyping equipment, such as the Fab@home plotter, has contributed to the development of novel scaffolds for bone tissue engineering. In this study, we report for the first time the use of a Fab@home plotter for the production of 3D scaffolds composed by beta-tricalcium phosphate (β-TCP)/alginate hybrid materials. β-TCP/alginate mixtures were used in a proportion of 50/50% (w/w), 30/70% (w/w) and 20/80% (w/w). The printing parameters were optimized to a nozzle diameter of 20 Gauge for the production of rigid scaffolds with pre-defined architectures. We observed that, despite using similar printing parameters, both the precision and resolution of the scaffolds were significantly affected by the blend's viscosity. In particular, we demonstrate that the higher viscosity of 50/50 scaffolds (150.0 ± 3.91 mPa s) provides a higher precision in the extrusion process. The physicochemical and biological characterization of the samples demonstrated that the 50/50 scaffolds possessed a resistance to compression comparable to that of native trabecular bone. Moreover, this particular formulation also exhibited a Young's modulus that was higher than that of trabecular bone. Scanning electron microscopy and fluorescence microscopy analysis revealed that osteoblasts were able to adhere, proliferate and also penetrate into the scaffold's architecture. Altogether, our findings suggest that the Fab@home printer can be employed in the manufacture of reproducible scaffolds, using a formulation 50/50 alginate-β-TCP that has suitable properties to be applied as bone substitutes in the future.

Multiplex PCR/liquid chromatography assay for detection of gene rearrangements: application to RB1 gene

Screening for large gene rearrangements is established as an important part of molecular medicine but is also challenging. A variety of robust methods can detect whole-gene deletions, but will fail to detect more subtle rearrangements that may involve a single exon. In this paper, we describe a new, versatile and robust method to assess exon copy number, called multiplex PCR/liquid chromatography assay (MP/LC). Multiple exons are amplified using unlabeled primers, then separated by ion-pair reversed-phase high-performance liquid chromatography (IP-RP-HPLC), and quantitated by fluorescent detection using a post-column intercalation dye. The relative peak intensities for each target directly reflect exon copy number. This novel technique was used to screen a panel of 121 unrelated retinoblastoma patients who were tested previously using a reference strategy. MP/LC correctly scored all deletions and demonstrated a previously undetected RB1 duplication, the first to be described. MP/LC appears to be an easy, versatile, and cost-effective method, which is particularly relevant to denaturing HPLC (DHPLC) users since it broadens the spectrum of available applications on a DHPLC system.

Ultrapure water for liquid chromatography–mass spectrometry studies

Improvements in trace enrichment techniques combined with the sensitivity of mass spectrometry offer enhanced opportunities to analyze ever lower concentrations of drugs, metabolites, pesticides or environmental pollutants. To perform HPLC and liquid chromatography-mass spectrometry (LC-MS) analyses under optimum conditions, the water used for mobile phase preparation needs to be highly purified and delivered on demand. Indeed, both UV photodiode array detection and MS detection methods are sensitive to organic contaminants (total organic carbon, TOC), and the water quality has a direct impact on the achievable detection limits. The benefits of UV photooxidation on TOC reduction for LC-MS studies were highlighted using electrospray ionization MS detection by comparing HPLC-grade bottled water, freshly produced UV185/254-treated water, and freshly produced non-UV-treated water.